Download XPMPro 2.0 User's Manual - Organic Semiconductor Group Dr. Trixler

XPMPro 2.0
User's Manual
Document version 1.0.0
Last modified 11/05 /2008
XPMPro 2.0 User's Manual
Table of Contents
Table of Contents
XPMPro User's Manual................................................................................................................1
Introduction...................................................................................................................................5
Installation.....................................................................................................................................7
Upgrade from SPM32...........................................................................................................10
Image processing on additional computers...........................................................................10
Initial Setup..................................................................................................................................11
Options..................................................................................................................................12
Stored parameter files..................................................................................................12
Scale bar and color scale..............................................................................................12
Default Size..................................................................................................................13
Graph Settings..............................................................................................................13
dataSAFE.....................................................................................................................13
ACQ window........................................................................................................................14
DSP tab........................................................................................................................14
Gains tab......................................................................................................................16
Scanner tab...................................................................................................................17
Closed-loop scanning...................................................................................................17
Operating Modes..........................................................................................................19
Define tab.....................................................................................................................20
Scan Settings................................................................................................................21
dataSAFE.................................................................................................................22
Input tab.......................................................................................................................22
Scan tab........................................................................................................................23
ACQ status bar.............................................................................................................25
Coarse Approach.........................................................................................................................26
Navigation window...............................................................................................................27
Aux Feedback..............................................................................................................27
Spec Location...............................................................................................................28
Tip Approach...............................................................................................................28
Tip control tab..........................................................................................................31
Advanced approach settings.....................................................................................34
Configuring approach motors..................................................................................36
Kinetic approach systems......................................................................................36
Stepper motor........................................................................................................38
Omicron 8 channel MSCU....................................................................................39
Omicron 3 channel microslide controller..............................................................41
RHK PMC100.......................................................................................................41
Inchworm(TM)/TTL.............................................................................................42
Attocube motor......................................................................................................43
PPC200 USB controlled piezo positioning controllers.........................................43
Starting an approach.................................................................................................44
Tip Track......................................................................................................................45
Manual control.............................................................................................................45
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Table of Contents
SPM Status...................................................................................................................46
Initial Acquisition........................................................................................................................47
RTAW toolbar......................................................................................................................48
Image manipulation and color table dialog...........................................................................49
Navigation window...............................................................................................................50
XY Graph window................................................................................................................56
Layout tab....................................................................................................................57
Curves tab....................................................................................................................58
Point spectroscopy................................................................................................................60
Output tab.....................................................................................................................61
Ramp subsection..........................................................................................................62
Control tab...................................................................................................................63
Advanced modes tab....................................................................................................65
Time Spectrum tab.......................................................................................................67
Point spectroscopy locations........................................................................................69
Spectrum Analyzer...............................................................................................................74
Oscilloscope .........................................................................................................................76
Alternative Imaging Modes..................................................................................................76
Multiple parameter imaging (MPI)..............................................................................76
Automatic parameter incrementing (API)...................................................................79
Analysis and Processing..............................................................................................................82
SM4 file format.....................................................................................................................85
Interactive histogram equalization........................................................................................88
Cursor Modes........................................................................................................................90
Data Analysis........................................................................................................................93
Processing.............................................................................................................................98
Processing images in Fourier space...........................................................................101
Three-dimensional rendering..............................................................................................103
Exporting data.....................................................................................................................105
Advanced Techniques...............................................................................................................107
Increasing resolution...........................................................................................................110
Variable gap spectroscopy..................................................................................................111
StabiliDrift..........................................................................................................................112
Conductance measurements................................................................................................114
Barrier height measurements using I-z spectroscopy................................................115
Barrier height measurements using a lockin amplifier..............................................116
Measurement parameters...........................................................................................117
Input/Output line-by-line imaging......................................................................................118
Force setpoint when using a commercial AFM..................................................................119
Changing the setpoint force using the setpoint knob.................................................121
Changing the setpoint force using the bias knob.......................................................122
Handshaking.......................................................................................................................123
Lateral drift correction........................................................................................................124
Vertical drift correction......................................................................................................126
Tip tracking of a feature......................................................................................................128
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Forming a panorama view in the NAV window.................................................................129
Manipulation and Lithography...........................................................................................129
Appendices.................................................................................................................................133
SM4 Data File Format........................................................................................................134
DSP Scan Board Commands..............................................................................................149
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Introduction
Introduction
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Introduction
XPMPro 2.0 is a new version of RHK SPM control software. Commonly, it is used to control
SPM100 electronics from RHK Technology. It features advanced acquisition capabilities,
sophisticated data processing algorithms, and superior manipulation and lithography controls.
This software includes all of the feature gained through 13 years of development on SPM32 and
several years of the development on XPMPro. Compare with the XPMPro, it has the following
improvements and enhancements:
●
Look and Feel. XPMPro™ 2.0 has had a face lift and reorganized controls to make the
operation more intuitive, enabling even beginning users to access and utilize the
advanced functionality that has made XPMPro the favorite of advanced researchers.
●
Dynamic Data Oversampling. When enabled, acquisition boards will run at their
maximum sampling rate and average all readings between pixels. At present XPMPro
only takes one reading per pixel. Oversampling will yield better S/N, especially when
scanning slowly
●
Spectroscopic Drift Correction. When enabled, the software will automatically correct
for drift in all three axis between multiple spectroscopy curves taken at the same
location. At present XPMPro can correct for drift between curves only in the Z axis.
Exact location of spectroscopic measurement will be stored with each curve
●
Workspace Sessions. This function will save all open windows in the DAW and store
them in one file, called a session. When you reopen that session, all windows will return
to their original position so you can start where you left off processing and analysis. This
session file can also be emailed to collaborators
●
Oscilloscope. The maximum number of samples increased from 256k to 1 MS. Data can
be acquired while utilizing Drag/Move Tip functions and during Pulse operation. Also
settings for using this option have been moved to the oscilloscope window for easier
operation
●
Time Spec UI implementation. This new spectroscopy acquisition mode allows the user
to program an experiment where any two parameters, such as Z position and bias voltage
can be ramped between end points at any predefined rate, stay at the end point for a
predefined period (dwell time), and then continue to the next set of end points, all the
while collecting data on any number of input channels. Ten steps in this process can be
programmed to be automatically acquired at any number of points in an image
●
Spectrum Analyzer. Settings controls attached with window, and the maximum number
of readings has been increased to 8,192k, providing 50 mHz resolution with a bandwidth
of 125 kHz. Optional acquisition module provides up to 2 MHz sampling. It displays the
average spectrum in real-time, which provides higher speed and resolution. Furthermore,
all settings have been moved to the Power Spectrum window for ease of operation.
●
Feature Tracking and display. When using the feature tracking capability, the position
of the feature on the surface is recorded as a function of time. A new display mode
allows this position to be shown as a function of time or displayed overlaid on the image
where it was acquired
●
Improved Atomic Manipulation. Dropped atomic features during manipulation
routines are no longer a problem. RHK has improved upon its previously released design.
The updated atomic manipulation routine improves productivity by up to 100 fold by
quickly and automatically locating lost features.
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Installation
●
High Speed acquisition module. A new optional module allows acquisition to be
acquired at up to 2 MHz on each of two channels. In additional to allowing faster
imaging, the higher bandwidth can also be utilized by the oscilloscope and spectrum
analyzer functions. This module can be added to any existing SPM1000 system running
XPMPro Version 2.0.
●
Increased scan speeds. The software has been optimized to allow much faster data
acquisition. For example, up to twelve images of 128x128 resolution can now be
acquired per second (six images in each scan direction).
●
Average spectroscopy curves in real time. This function displays the running average
of all curves taken at each point in real time in additional to the display of each
individual spectroscopy curve.
●
Real-time processing and display of spectroscopic data. In addition to showing the
raw data for each curve, real-time display of calculated derivative and/or second
derivative can also be shown.
●
Redesigned Analysis and Processing software. The analysis and processing sections of
the software have been upgraded to provide much faster and efficient processing and
visualization.
●
Integration of PLLPro into XPMPro. Tight integration of the PLLpro into XPMPro
greatly improves ease of use.
●
PMC100 integration into XPMPro. All configuration functions of PMC100 are now
set inside of XPMPro instead of through separate application
Customers upgrading from SPM32 and XPMPro will recognize most of the features and enjoy
an easier to use interface through a reorganization of controls as well as a polished GUI made
possible by the Windows OS.
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Installation
Installation
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Installation
Please see the Installation Guide Video (screenshot show below) on the RHK website for
instructions on all aspects of installing your new XPMPro 2.0 software.
http://www.rhk-tech.com/xpmpro_2.0.php
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Initial Setup
Initial Setup
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Initial Setup
When the program is started, it will check for the presence of the sentinel key on the parallel port
of the computer This is the same protection key used to authorize SPM32. For existing users, an
upgrade password will be required to activate the key for XPMPro If the key has been activated
for XPMPro, the
program will try to
connect to the SPM100.
This will fail because
the IP address of the
SPM100 has not been Figure 1 Screen shot of XPMPro main window
entered into the
software yet. The
screen will then display the main tool bar as shown in Figure 1.
Options
The OPT menu can also be used to unlock additional features of the software that require an
extra password. At this time, the only additional module is the high speed scanning option
provided by the Data Translation DT9832 USB adapter. This menu is also used to access some
universal parameters that apply to both the acquisition window and the analysis and processing
menu.
Stored parameter files
Click the OPT button to open a menu where different parameter files can be opened. The PRM
files store all of the settings in the program. The ability to switch PRM files allows multiple
systems to be operated from a single installation. Piezo calibrations, stored spectroscopy
experiments, etc. are kept in the PRM file and can be individually maintained. Since the new
SM4 file format contains the complete PRM file inside its file header, an experiment can be
recreated from the stored data file by choosing to read the parameters out of the stored data file.
This is accomplished by choosing Read PRM from SM4 file. Note, this is only possible from an
SM4 file saved with XPMPro 2.0 and above. An SM4 file converted from an existing SM3 file
will not have the parameters stored in it since that feature was not available as part of the SM3
format specification. After choosing this menu option, click on the desired SM4 file in the file
browser. An alternative method of importing settings from a saved file is to choose the menu
item DAW Page and then click on an open data window in a the DAW. This will retrieve the
PRM file from the saved SM4 file associated with this data. The third option for changing
parameter files is the traditional way of directly browsing for a different PRM file using the
standard file browser. We also can store the working parameter to a prm file at the folder that we
want.
Explore folders
Shortcuts to the working folder and support folders are added to the options. The install folder of
XPMPro 2.0 can be easily found by these shortcuts. Also the electronic version of the supporting
files also can be easily found by these shortcut.
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Initial Setup
ACQ window
Figure 2. Screen shot of real time acquisition window
Open the acquisition window by clicking on the ACQ button. The window will appear as shown
in Figure 2. The first important step is to enter information about the scan head and the SPM100,
which is located at setting->configure hardware. At hardware tab, selects experimental hardware.
Other tabs are detail introduced in the following text.
DSP tab
The IP address of the SPM100 needs to be changed so the PC and SPM100 can communicate
correctly. The address is entered by choosing the menu item Settings/Configure Hardware to
popup the hardware settings window which is shown in Figure 3. Enter the appropriate
SPM-100 IP address in the box so the SPM100 is in the same subnet as the PC. For example, if
the PC address was assigned as 192.168.10.1, then 192.168.10.2 could be entered here. The first
three sets of numbers have to be the same for the PC and SPM100 to communicate, but the last
number must be different. The Debug Status can be set to Normal. The other choices should
only be used if instructed to do so by RHK as a diagnostic step. If Extended Debugging to file is
chosen and the software is left running for a long time, enough messages can be written to the
hard drive to completely consume all free space. If a hard drive ever gets filled up for no
apparent reason, check this setting to see if it is set incorrectly. The file written when debugging
is turned on is called RHKDEBUG.TXT and it will be in the same directory as XPMPro is
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installed.
The Serial Number should be left at 0 unless multiple SPM100s are installed in the lab and they
are all located on the same LAN instead of using a second network board in the computer as
recommended. If a second board is not used, then all SPM100s will be reachable by all
computers. If more than one is started at the same time, the computer may assign its designated
IP address to the wrong SPM100 which will create problems since the ADC board is not
connected to that SPM100. The computer can be guaranteed to always connect to the correct
SPM100 by entering its serial number here. In this case, the computer will only assign the IP
address when the SPM100 with this serial number requests an address. All other requests will be
ignored. When set to zero any IP address request will be answered, but if there is only one
SPM100 that will ever reach this PC, it can be left at zero for simplicity.
The SPM-100 Scan Code is the software downloaded to the DSP board when it is initialized by
the program. The board itself
only has enough code in its
ROM to boot and then
receive the actual operating
code from XPMPro This
makes upgrading the boards
in the field quite simple.
New features can be added
to the board and they will be
contained in the code. If an
upgrade is sent from RHK,
the COF file should be
placed in the installation
directory and the new name
entered here.
DSP Hardware and DSP
Software are status displays
that are read from the
SPM100. This allows an
easy and convenient place to
determine the COF version
and hardware kernel version
of the SPM100 DSP board.
Figure 3: Screen shot of DSP tab
The hardware diagnostic
section presents various measures of performance and may provide valuable troubleshooting
information if the program halts intermittently or other problems appear. The values should be
recorded before contacting technical support as they can help diagnose the problems.
If communication problems appear that don't seem to make any sense after double checking the
cables and IP Addresses, try checking the Use Reduced Packet Size box. Certain Virtual Private
Network (VPN) and secure communications software automatically split TCP/IP packets into
smaller pieces in order to encrypt them. Since the SPM100 and XPMPro are expecting to
communicate in packets of a fixed size, the smaller packets will not work between the two. If
this gets checked and works, the only trade-off is the number of arbitrarily defined spectroscopy
points that can be used within any single image is reduced.
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Gains tab
The preamp gain and high voltage amplifier gains are set in the Gains tab (Figure 4). Internally
the signals are all limited to +/- 10 V. To properly calibrate and record all settings, XPMPro
must know the physical signal with respect to the internal voltage. The proper conversion factor
is entered here. For a high voltage unit where the maximum output is 215 V, the gains should all
be set to 21.5. For a low voltage
unit, the gains are equal to 13.
Other factors are possible
depending on the setup of the
head. Whatever voltage is
applied to the head compared to
the internal 10 V signal needs to
be entered here. Two other
common situations are using the
SPM100 with the RHK HVA900
which has a maximum output of
450 V. In this case, the gains are
45. The second is if the optional
0-10 V board is installed which is
used to drive a closed loop stage
from a third party, the correct
value here is 0.5.
Newer SPM100s have the gain of
the high voltage outputs
programmed into the EEPROM of
the unit. If no modifications have
been performed to the unit since it
left the factory, the Use values
stored in SPM100 can be
Figure 4: Screen shot of Gain tab
checked. This prevents the gain
values from being changed
accidentally which would subsequently change the scan head calibration.
Unless the sample bias output from the SPM100 is externally amplified or attenuated, the gain of
the bias should always be one. If the bias out put is externally amplified or attenuated, here
should be amplification number or attenuated fraction. The STM Current per monitor volt
depends on the overall preamplifier gain. A gain of 108 would mean 10 nA/volt. A gain of 109
would mean 1 nA/volt. If this value is entered wrong, then all recorded currents (tunneling
conditions, spectroscopy readings, etc.) will be incorrect but can easily be scaled later if the
value entered here when the data was acquired is known. If it is easier to think of the current
calibration factor in terms of a gain factor, the correct value can also be used in the Preamp gain
entry box. This will be the inverse of the setting directly above it and changing one
automatically changes the other.
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Scanner tab
The actual calibration values for the
particular scan head in use are entered
in the scanner tab shown in Figure 5.
A text description for the scan head
can be entered in the Scan Head
Description. The amount of motion
per piezo volt for each direction is
entered in the correct box. If there is
only one piezo that provides both
offset and scan, then Offsets summed
with scan should be checked. If one
piezo element is used for scan and a
separate one for offset, then this
should be unchecked and the correct
calibration values entered for the
offset piezo element.
An accurate calibration of the scan
head will only be possible once
images of a known standard are
obtained. However, if an approximate
value is known ahead of time, it is
Figure 5: Screen shot of scanner tab
worthwhile to enter it when starting
so the scan size is close to the correct
value. Confusion can occur if the calibration is not changed and the scan head has a dramatically
different scan calibration than the defaults. Interpreting an image supposedly taken over an area
of 10 nm when it is actually covering an area of 200 nm can cause the user to miss small features
that are expected to be visible.
Closed-loop scanning
The outputs from position sensors (capacitance, laser interferometers, etc.) can be connected to
the rear panel DSP ADCs, and the scan output voltages are then continuously adjusted to
maintain an exact position. This insures that the displacements are truly linear and no piezo
nonlinearities or thermal drift are present in the data. For example, as the stage shifts due to
thermal effects, the output of the position sensors will change and the DSP board can then
change the scan output voltages to maintain the correct position. Also, as an image is scanned, if
the next pixel is supposed to be 2.33 nm away and the voltage returned from the stage indicates
it moved 2.37 nm, the DSP board will reduce the output voltage to the appropriate amount until
the displacement is exactly 2.33 nm.
This type of system relies on feedback so a bandwidth must be selected in order to insure proper
operation. The location must not be sampled too frequently or the feedback system will try to
correct the displacement too often and an unstable feedback loop will be present. When scanning
an image, the bandwidth of the closed-loop circuit should be at least a factor of 10 larger than
the scan speed. Otherwise, the DSP board will not have ample opportunity to make small
corrections before the image data is acquired and the tip is moved to the next pixel. This factor
would provide the scan board the chance to apply about 10 corrections to the displacement as the
image data is acquired. The bandwidth must also be below the resonant frequency of the scan
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stage or oscillations will occur. Most stages have a fundamental mode of less than a kHz or so.
Therefore, many users will have to reduce the image scan speed to take advantage of the closed
loop capabilities.
The calibration of the closed loop sensors must be carried out and the appropriate scale factors
then entered into the software. A known grating should be scanned and after the features are
measured, the known dimensions are compared to the output voltages from the displacement
sensors to provide a distance/voltage calibration. The second way to calibrate the position
sensors is with the automatic calibration feature. The DSP scan board performs a series of scans
with specified dimensions and the output of the sensors measured with the ADC1 and ADC2.
Since a known distance was scanned, the sensor output per distance can be calculated and the
calibration factors will be automatically entered into the software in the advanced feedback tab.
Note that when XPMPro sets up the measurement series, it relies on knowing the position of the
front panel X Scan Range knob in order to specify the scan size to the DSP board. The sensor
calibration factors are therefore dependent on the X Scan Range knob position. If the
range knob is turned (to increase or decrease the available scan area) the automatic
calibration routine MUST be performed again.
Feedback tab
The parameters that determine the
performance of closed-loop scanning
are entered in the feedback tab as
shown in Figure 6. Turn On Enable
positioning feedback for scanning to
proceed under closed loop control. All
piezo nonlinearities and drift should be
eliminated. Do not activate this feature
unless the position sensors are properly
connected and the full concept of
closed loop scanning is completely
understood as improper usage can
result in scan head damage. After
connecting the outputs of the sensors to
the rear panel ADC inputs, turn on
Position sensors connected Be sure
to use DSP ADC#1 for the X axis and
DSP ADC#2 for the Y axis. The Time
constant / Bandwidth parameter
should be adjusted to set the
performance of the closed-loop sensor
Figure 6: Screen shot of feedback tab
circuit. Since there is an inverse
relationship between the two, setting
either of them determines the other. The user can set whichever one is more comfortable to think
about. Click the Calibrate button to perform the automatic calibration routine. If at a later time,
the calibration should be checked, simply click Recalibrate If a manual calibration was
performed by scanning a known reference and measuring the nonlinearities, they can be entered
in the next three parameter, X(Y) size ratio and XY Angle correction
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Advanced Feedback tab
Increased precision can be gained by
applying higher order corrections to
the closed-loop scan algorithm. If an
automatic calibration is performed
the extracted characteristics will be
automatically entered here. The tab
is shown in Figure 7. If the position
sensor does not read exactly zero
when there is no physical
displacement, enter the voltage offset
in. The voltage output from the
sensor as a function of displacement
is specified by X/Y detector offset.
X/Y detector sensitivity. Ideally the
position sensors are perpendicular
and independent of each other,
however in real systems many times
there is crosstalk between the two
directions (a displacement precisely
along the X axis also changes the
voltage output of the Y sensor a
small amount.) and the relative
crosstalk is determined by the
Figure 7: Screen shot of advance feed back tab
Detector cross coupling parameter.
Nonlinear terms in the sensor output voltages can be specified with the XY square & cube
sensitivity settings.
Operating Modes
The proper operating mode that the SPM100 will be in is important in order to have the feedback
signal labeled properly and to preset certain other conditions in the software. The mode is
selected by choosing Settings/Operating Modes to open the window shown in Figure 8. Two
important modes integrate the PLLPro into XPMPro. When using the PLLPro under typical
conditions, the best choice is PLLPro Master. Once this is selected, it will automatically start the
standalone PLLPro control program and setup a communication process so the software can
exchange information with the PLLPro program. If the PLLPro software is already running, it
should be exited to allow XPMPro to call the PLLPro program. This insures the proper
interprocess communication system is setup.
It is important to have the PLLPro properly connected to the SPM100 so the correct channels are
measured and associated with the correct signals. The window provides a hint for connecting the
two together since it grays out certain channels in this mode. It does this by querying the PLLPro
for the channel labels, units, and conversion factor for the DAC outputs on the PLLPro rear
panel. It is important to have the PLLPro DAC1 connected to the Feedback Input connection on
the SPM100 back panel. The other three connections should be DAC2 to AUX4, DAC3 to
AUX5, and DAC4 to AUX6. Once this is done, it will not have to be changed in the future and
even if the PLLPro operating mode changes, the PLLPro will take care of automatically sending
the appropriate signals out the correct DAC and also relay the labels and units to XPMPro so the
data channels have meaningful names as assigned inside the PLLPro software.
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The other entry named PLLPro User will not gray out any of the entries and is intended to be
used by advanced users who have setup the PLLPro to operate in a mode that is not
straightforward and requires manually entering the channel labels and units. XPMPro will still
gather status data and measure the signals from the PLLPro, but the physical interpretation and
connections between the two units have to be configured manually.
Define tab
Choose the acquisition
mode at the top of the box.
Selecting STM will set the
feedback signal label to
Current. If set to AFM100
then the feedback signal is
Force Error. Additionally,
Aux4 is changed to Normal
Force and Aux 5 is changed
to Lateral Force. Aux 6 is
labeled AFM Status and
needs to be connected to the
MUX1 output of the
AFM100. In order for the
AFM100 to be used
properly, the cables from
the rear panel outputs
MUST be connected to
these input channels.
Any arbitrary string can be
used for the feedback signal
Figure 8: Screen shot of operating mode setting
if User is chosen. The
channel will then carry the
label entered in the User entry box below. The units and appropriate calibration can also be
entered here so the acquired data has the correct label as well as meaningful units. An example
of this mode would be non-contact AFM in vacuum where the change in frequency between the
free oscillation and when interacting with the surface is the feedback signal. In this case, delta F
could be entered as the label with the units set as Hz and the units/input volt depending on the
settings of the external electronics that converts the frequency shift into a voltage.
If extra channels are going to be acquired during imaging or spectroscopy, they should be
applied to one of the SPM100 rear panel auxiliary channels. The label of the channel can be any
arbitrary string and the units and calibration can also be entered here. Examples of signals to
acquire are Lateral Force (in contact AFM), Conductance (in STM), Barrier Height (in STM),
Dissipation (non contact AFM), Phase (non contact AFM), etc.
DAC/Locks tab
Due to the multifunction of our SPM electronics, the DAC output can be used in many functions.
In this tab, the DAC out can be lock to some certain function to avoid the cross talk between
different measurements. The DAC can be selected to lock to special channel in the Locked IO
channels panel. The functions that set the DAC as the output channel can be read in the DAC
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assignment panel.
Count tab and AFM tab
Some of user may use the counter to count the photon or electron for the measurement. The
setting of the counter can be set at count tab. The main parameters are the count interval and
some display parameters.
When we use AFM mode, AFM detector parameters are set here. They are vertical force spring
constant, deflection sensitivity,
lateral force constant, lateral
deflection sensitivity, laser current
gain, laser photocurrent gain, PSD
thresh hold, or some external signal
parameters. (given the typical value
of these parameters)
Scan Settings
The main parameters that effect
data acquisition are accessed from
the Scan menu item of the Settings
menu. The initial data directory and
file naming convention is entered in
the Save/Display tab (Figure 9).
The Scan Count is the number of
images to acquire before stopping
the data acquisition. A value of zero
means free scanning which will
continue until stopped manually.
Place a value here to scan a
predetermined number of images if
it is undesirable to continue
scanning after some unattended
experiment has completed. If, for
example, Scan Autosave was on to
write all images to disk, but it was
desired to only take data for a few
hours instead of a long period of
time a number can be used here to
stop acquiring data after this
number of scans has been taken.
There are two imaging modes in
XPMPro. The first one is called
Figure 9 Screen shot of scan setting
Normal and it is identical to the
manner in which SPM32 acquired
data. Each set of data acquired during one trip across the surface and back is displayed after that
line is finished. Any changes in parameters (tip location, scan speed, etc.) are sent to the
SPM100 after that line and take effect immediately. This is also the mode required to stop at
predetermined pixels and acquire spectroscopic data. If this mode is chosen then a Scan Delay
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will occur at the end of the frame before the next frame starts. If the tip needs to quickly return
from the bottom of the frame to the top of the frame, this delay allows piezo creep to decay so
the first few lines of the subsequent frame do not show distortion. Another useful feature of this
delay is when acquiring an automated series of images in unattended mode. The delay can be
used to allow a large amount of time to elapse before the next image is acquired in order to give
the system plenty of time to reach a new equilibrium or have some slow process occur while
capturing a “before” and “after” image. Movie mode simply takes the data as rapidly as possible
with no stopping between lines to update parameters etc. It also prevents stopping the scan in the
middle of a line to perform spectroscopy measurements. It is most useful if an experiment
requires the maximum possible data acquisition rate in order to capture dynamic processes
occurring on a short time scale. There is also no pause at the end of the frame to update the
entire screen, instead data acquisition keeps going in the background and the data will be
displayed when the computer is ready to update the screen for the next image. The overall
difference in acquisition rate can be dramatic. If scanning a 128x128 pixel image at 1 ms/line,
normal mode could acquire about 2 frames/second Movie mode, on the other hand, could
acquire closer to 7 frames/second.
The Direction is used to choose whether scanning occurs along the x axis or y axis. This can
also be changed using either the F7 key or pressing the toolbar button on the acquisition
window.
An alternative method to prevent creep from distorting the first few lines of an image after the
tip is rapidly returned to the upper right corner of the scan frame is to start the next frame from
the end point of the last frame. This means an image will be acquired from the top of the frame
to the bottom and the next frame will be acquired from the bottom of the image to the top. Place
a check in Alternating Slow Scan to use this feature. To obtain a series of scans over the exact
same part of the surface (ignoring thermal drift effects), Slow scan disabled should be checked.
This can be useful to acquire data for comparison within the same image while changing some
external parameter (such as AFM load) or to use as a diagnostic when first setting up image
acquisition while optimizing the feedback conditions.
The Standby Action is used to select what the scan head should do when image acquisition is
not taking place. The options are to be at rest in the upper right corner of the scan frame, to be at
rest at the center of the scan frame, to be at rest at the center of the piezo range, continuous
scanning of the first line or continuous scanning of the entire frame. Piezo creep can be
minimized if the scan piezo is always in motion repeatedly scanning over the same part of the
surface since there is no time when it is at rest and therefore “relaxes”. Choosing scanner zero
can be helpful with the RHK UHV350 AFM since the PPC150 can be switched from one
direction to another with no adverse effects. If the voltage to the scan head legs is zero and they
have no deflection, there will be no abrupt jerk of the head when the PPC150 is switched.
If a scan head is in use that has a resonant frequency which gets excited by the harmonics of the
conventional triangular waveform, this can be avoided by changing the Scan Type to sinusoidal
instead of linear. Now the scan head decelerates as it approaches the end of the line and
accelerates gently after turnaround. This avoids transients in the scan head which could cause it
to “ring” after abruptly stopping and turning around to move in the other direction.
To reduce noise multiple ADC readings can be averaged together and the result then be
considered the value for that pixel. To activate this feature click the Oversampling checkbox in
the window. The slower the line time, the more averages that can be acquired before the next
pixel location is reached. As the Line Time or Scan Speed is changed, the number of samples
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will be automatically updated in the information box. A maximum of 1024 readings can be
averaged together. Once this value is reached, slowing the scan down more does not reduce the
noise further.
Save Tab
Figure 10 is a screen shot save tab. A
Default Saved Path is chosen using
the Select button and browsing to the
directory where all data should be
stored. A default comment can be
entered by clicking on the Comment
button and typing in a string of up to
256 characters. This can be used to
record conditions related to sample
preparation or various other
experimental parameters that are
relevant to interpreting the data
correctly, but would not be something
the software measures from the
SPM100.
When Save Autoname is checked, the
files are named automatically when the
save button is pressed during an
image. A useful feature of the
XPMPro naming method is the use of
a root and an index to automatically
generate unique names for each piece
of data. The root is the first part of the
name and can be any arbitrary length
since Windows XP and 2000 can
understand long filenames. The index
is then incremented after each file. For
each character of the index that is a
number, it starts at zero and
increments up to nine. For each
character that is a letter, it will start at
A and increment up to Z. The number
of characters entered in the index
Figure 10: Screen shot of image save tab
determines the number of unique
filenames possible. For example, if the index was entered as 0, there would only be 10 possible
names. If the index as entered as 00, there would only be 100 possible names. If the index was
entered as A, there would only be 26 possible filenames. For the example shown in the figure,
the possible names are 234,000 (10x10x10x9x26). The first one would be OUT0001A.SM4 and
the last one would be OUT9999Z.SM4. The files automatically get the extension SM4 which is
the file format XPMPro is using to store data. This format is a superset of the SM2 file format
SPM32 used to employ.
If Comment Question is checked then as each file is saved, a dialog box to type in a comment
for this particular file will be presented. This provides the opportunity to enter unique comments
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for each file when desirable. Be careful about having this checked though because saving will be
halted until the dialog is filled in. Do not activate this and expect to automatically save data in an
unattended manner.
It is possible to automatically save every scan acquired without user intervention. Placing a
check mark in the Scan Autosave box will save each file to the hard drive with the proper name
as determined by the root and index. This feature allows a long series of related images to be
saved in unattended fashion.
At the end of each image scan, the color mapping of z values to colors can be adjusted to best fit
the data. Activate this feature by checking Autoscale Image. Occasionally this may cause the
color map to be worse than before if a single spike is present in the data that skews the
maximum z value far from the rest of the data. If this is unchecked then the remapping will only
occur when manually requested via the F5 button or the Autoscale button on the toolbar.
In customary GUI standards, the Apply button will save the parameters to the PRM file and
have them take effect but leave the window open. The OK button will save the parameters to the
PRM file and have them take effect while also closing the window.
dataSAFE
A revolutionary new feature of XPMPro is the ability to periodically save a scan during the
acquisition to prevent loss of important data in case of a power outage. The user can choose
where to store the temporary files with the Temp Folder Path parameter. To recover a partial
scan, the data analysis window can be opened and the temp folder browsed to locate the temp
files. Each one is saved with a unique name generated by the date, time, and extra numerical
string. All valid data will be displayed as normal and the values for the region of the scan not
completed yet are set to zero so that part of the image will look completely flat. The periodic
saving is active under two conditions. If the Enable check box in the Line section is checked
and if the total acquisition time for the scan exceeds five minutes. The frequency to save data is
entered next to the check box by specifying how many lines of data to acquire before writing the
file. This is great protection from power failures; after all, a partial piece of important data is
better than losing the entire scan.
Be sure to understand the difference between the ring buffer and Scan Autosave. If the second
one is checked, then every file is written to the current save path using the filename formed by
the root and index parameters and will never be overwritten by XPMPro. If Scan Autosave is
not on but the image dataSAFE check box is marked then the complete scan will still be saved to
the temp path and can be recovered until overwritten. By using the DAW file browser, any file
can be transferred to the save directory by right clicking on the name and choosing Move File.
This will be covered in more detail later.
Input tab
To select which channels should be acquired during a scan across the surface, the Input tab
(Figure 11) is used. Any channel that has a check mark in the Image column will be sampled at
each pixel to form an image. Note that the names of the channels will be whatever was entered
in the Operating Modes/Define tab discussed above. If an experiment is taking place where it is
desirable to record a signal that does not vary any during the time scale of the scan, then the
check box in the Status column should be checked. When this is done the channel is measured
once at the end of the scan frame and the data is stored in the file header for a permanent record
of the signal level during the image. The most common example of this would be to record the
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analog output of a temperature meter so the actual temperature is recorded for that data set.
There is no need to form a a two dimensional image of temperature because it varies so slowly,
the same value would be recorded at nearly every pixel. The voltage can later be displayed using
the Page Info command discussed in a later chapter.
The pixel resolution is also selected
here. The Ganged button can be
checked to acquire images with an
equal amount of pixels and lines. In
this case, only the Points per line
can be selected and Lines per
Frame is automatically set to the
equal value. If separate is checked,
then the Points per Line and Lines
per Frame can be chosen
independently. Both values are
restricted to numbers that are a
power of two and range from 8x8 to
8192x8192.
Record one scan direction should
be checked if the data is only
needed during the forward scan
across the surface. This can save
time and file size by eliminating
data pages and also the amount of
time it requires to take data while
moving across the surface in some
circumstances.
The ADC gain is set for each
channel in software. The DT3016
board has programmable gain that
can acquire 16 bit resolution data
and have it spread over a 20 volt
range (0.305 mV LSB) or as small
as 2.5 volt (0.0381 mV LSB).
When the range is turned down, this
increases total sensitivity to provide
effectively 19 bits of resolution for
Figure 11:Screen shot of input tab for scan setting
all channels except Topography.
The total sensitivity for that channel
has additional gain from the SPM100 Z Position Gain knob which amplifies the signal before it
is sent to the DT3016 board. If the Z Position Gain knob is at 128 and the signal is still very
small, increased sensitivity to small corrugation can be obtained by increasing the gain on the
ADC board through software using this panel.
To obtain better resolution on the other channels, the gain should be increased until it reaches a
point where the signal would saturate the ADC. For example, if a tunneling current of 100 pA is
in use, this corresponds to 100 mV signal (assuming 109 gain). Since the signal will rarely
exceed even 1 volt (1 nA) the range of the current channel could be changed to +/- 1.25 V so it is
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possible to detect variations in current with better resolution.
ACQ status bar
The lower part of the ACQ window contains a status bar with a great deal of information. The
appearance of this bar can be altered to each user's taste. Various panes can be hidden or they
can be highlighted by changing the colors used within that pane. Each one can also be resized to
fit the amount of text contained in that part. To customize the colors, right click on the bar and
choose Customize to open the window displayed in Figure 12.
To hide any panel, un check the box on
the left side next to the name. The text
and background colors can be adjusted to
highlight specific panes. The DSP
Offline/Online is pre-configured to
change background as a specific example
of visually displaying the status using a
color clue for knowing with a glance if
communication is working. Individual
imaging modes are also colored
differently so it is simple to realize what
acquisition is taking place without
specifically reading the real text
contained in the status bar.
Instead of opening the main window,
each pane can be individually hidden and
configured by right clicking on that
particular pane and choosing to hide, set
the text color, or set the background
color. Once a pane is hidden, to display it
again the main configuration window
must be opened and a check box placed
next to the appropriate field.
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Figure 12: customize status bar
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Navigation window
The next step to data
acquisition is the requirement
to bring the probe and sample
close enough to create an
interaction for feedback. This
can be a tunneling current, a
cantilever deflection, a
frequency shift, etc. In most
cases some separate
mechanism or motor is used
to take large steps while the
software checks for tipsample interaction in between
each step.
The approach system is
configured through the
Navigation window which is
opened by clicking on the
NAV button in the main
launcher bar. When the
window is first opened, it will
appear as shown in Figure 13.
At the bottom of this window
is a set of panels that each
contain a title bar and a
double arrow control. Each
panel can be opened or closed
by double clicking on the title
Figure 13: Screen shot of navigation window
bar or single clicking the
double arrow. There are six
panes, but only three can be opened at a time due to limitations in the screen space. Whenever a
fourth pane is opened, one of the other three will automatically close.
Each pane is used for controlling a particular feature of XPMPro or to simply display
information. The panes are named Aux Feedback, Spec Location,Tip Approach,, Tip Track,
Manual Control, and SPM Status.
When using the dual monitor setup recommended by RHK, this window works nicely if placed
on monitor number 2 for easy access while imaging. Data acquisition can take place on one
monitor while the other one is used for navigation and scan control.
Aux Feedback
The AUX Feedback function will be covered in more detail in a later section, but it is usually
used to null out drift in the z direction due to thermal fluctuations. All of the settings as well as
the buttons used to produce coarse steps are contained in the Approach Control pane. If point
spectroscopy is to be acquired either within an image or by moving the tip directly from point to
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point, the locations can be defined using the Spec Location tab. This tool will be described in
more detail in a later section. The Tip Tracking pane can be used to configure a lateral dither of
the tip over a feature using the X and Y scan raster DACs. The DSP board will then monitor the
fluctuations of a signal and by measuring the local gradient it can adjust the center position of
the tip to stay above a feature on the surface. This is particularly useful to track diffusion of
adsorbates or defects on the surface as well as provide a measure of drift as a function of time.
The final pane is a display of all analog signal levels in the SPM100 as well as the two pulse
counting channels. This is updated at a rate of approximately three times per second. A large
number f readings are measured and averaged together to reduce the jitter in the readings.
Spec Location
Spec Location will be explained in great detail in a later section. It is used to select pixels within
an image to stop the scan and acquire spectroscopic data.
Tip Approach
To control and configure the
approach, open the Tip Approach
pane shown in Figure 14.
The approach mode and motor
settings are accessed by clicking
on the Motor Setup button in the
approach pane. It will open the
Figure 14: Screen shot of tip approach
window shown in Figure 15. The
first parameter is the Approach system which is determined by the physical motor used to bring
Figure 15: screen shot of motor set up
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the tip and sample together. The settings that determine how the chosen motor moves is
configured in the Motors tab described below. Many of the motor interfaces require a separate
electronics unit from RHK that XPMPro communicates with either through a network
connection or a TTL interface using a separate TTL board. It is also possible for the software to
interface to a few types of electronics supplied by a third party.
There are five different modes of synchronizing the SPM100 with the coarse steps. All of these
use the software as the master synchronization controller. The choice of what to use depends on
many factors such as delicacy of probe and the patience of operator. In most cases, the slower
the approach, the less likely to cause undesirable tip-sample contact once they get close to each
other.
Tip Retract mode is the safest and slowest method. The program fully retracts the probe, makes a
motion cycle, then with the feedback loop active, releases the probe, allowing it to approach the
sample. The software monitors the Z axis motion to determine if it stabilized above the threshold
value (defined as the percentage of full range the tip has been retracted). Depending on the
settings of the feedback loop’s gain and time constants, each cycle typically takes about 0.1
second. The tip retract mode is the preferred mode for STM operation to assure no tip sample
contact occurs when approaching. It is nearly impossible to have tip sample contact using this
mode because the tip ramps forward only as fast as the feedback loop “knows” it can stop before
contact occurs. Tip-sample contact can occur after approach is finished if the feedback loop gain
is too high and the head goes into a loop oscillation, however this behavior is independent of
selecting Tip Retract. If oscillation occurs, the tip and sample can contact because the oscillation
has a large enough amplitude that the z piezo extends larger then the nominal gap.
Feedback detect mode monitors the position of the feedback loop while the probe approaches the
sample. In this case, instead of extending and retracting the tip after each step, the tip is always
extended and the feedback loop is constantly monitored for a reaction to the surface. The motion
automatically stops when the Z position has been retracted past the threshold setting. This mode
is recommended for contact mode AFM where the tip will normally contact the sample and no
damage will be done to the cantilever due to its flexibility. This mode is also appropriate for
techniques that have long range surface interactions, such as NSOM. However, tip-sample
contact may occur using this mode. To avoid contact, the speed at which the tip approaches the
sample during a coarse step must be slower than the speed the tip can be pulled back by the
feedback loop, and this condition is rarely met in practical scan heads.
Signal detect mode is similar to the feedback detect mode except the software monitors the input
signal channel (current, force error, etc.) rather than the Z axis motion. The danger of the probe
crashing is less than for Feedback Detect, since the signal circuit responds faster than the
feedback loop. An STM preamp usually has a bandwidth of tens of kHz whereas a feedback loop
will typically only have a bandwidth of a few kHz. However, if avoiding a probe crash is of
prime importance, the Tip Retract mode is recommended. It is important to have the Signal
Threshold set below the setpoint knob value or a crash will occur because the approach will
continue even after the SPM100 is in feedback since the signal will still not exceed the threshold
until the z piezo is fully retracted and a crash occurs. The software monitors the position of the
Setpoint knob and given the calibration of the feedback signal in physical units, it will check to
make sure the threshold has been set to a value less than the setpoint knob. If this is not the case,
a warning message will occur providing the opportunity to either raise the setpoint or lower the
threshold.
Tip Retract/Signal acts like the Tip Retract mode discussed above in that it pulls the tip back and
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ramps the tip forward using the feedback loop of the SPM100 but instead of monitoring the Z
position level, it monitors the feedback channel and stops the approach if the level gets above a
threshold. It uses the same Signal Threshold parameter as the Signal Detect method.
Open Loop Ramp takes advantage of the fact that the bandwidth of most preamplifiers is larger
than the bandwidth of the feedback loop. Therefore, decreased approach times can be achieved
with this method. The feedback electronics of the SPM 100 is bypassed and the tip is ramped
towards the sample through direct control using the DT3016 card. The z piezo is ramped forward
very quickly between coarse motion steps, and the feedback channel is monitored for a non-zero
signal. The response time will depend on the bandwidth of the signal circuit. For STM, the
response can easily be as fast as 20 ms (50 kHz bandwidth setting of the IVP-PGA). When the
signal goes over a preset threshold indicating a response to the surface has been detected, the
ramp is stopped. The tip is then retracted and reapproached at a decreased speed to establish
feedback. Since the tip is ramped using the DT3016 card instead of the feedback loop, the
amount of time to extend/contract the z piezo between coarse steps is much shorter and the total
approach time is much less compared to using the feedback loop of the SPM100 to
extend/contract. An output ramp voltage is generated by the ADC card and applied to the
appropriate rear panel DAC output of the SPM 100. This BNC is attached to Z position
modulation input #1 and the waveform is then amplified and applied directly to the z piezo. The
ramp speeds and motion limits are set in the Advanced/Tip Ramp tab discussed below.
The rest of the parameters in this tab set the level when an approach should be considered done
as well as the timing and speed. The Approach Threshold is used during a Tip Retract or
Feedback Detect approach. The probe is advanced until the control loop stabilizes above the
threshold value. The range is -100% to +100%, where -100% is fully extended, and +100% is
fully retracted. A value of 0% would mean the probe advances until it is just past the midpoint of
the feedback range. Initially, this value should be set to something conservative like -50%. After
measuring the step size of the coarse approach relative to the total range of the Z piezo, this can
be set to something close to 0% to avoid manual adjustment (via the ‘+’ and ‘-‘ buttons) after
coarse approach in order to center the z piezo within its range. The smaller the coarse step size
relative to the total z piezo range, the closer this can be used to automatically center the z piezo
in its range when an approach is finished. If the coarse step size is close to the total z range then
this should be set to a large negative number to avoid taking one extra step which would cause
tip-sample contact if the z piezo has run out of range after that step.
When using Feedback detect or Tip Retract mode, Feedback delay sets the amount of time to
test if the position of the z piezo is above the threshold value. If the signal remains above the
threshold after this amount of time, the controller stops the approach and assumes it is complete.
As the feedback loop response time is lowered, this value should be set higher since the SPM
100 will require more time to extend the tip past the threshold while probing for the surface if
Tip Retract is used. Values as high as 5 sec. may be needed when the feedback loop is set very
low as typically used in NSOM. If the approach stops after a single step but the SPM100 still
shows no feedback signal, then this value needs to be increased in order to give the feedback
loop a longer time to extend the z piezo past the threshold.
When Signal detect is chosen, the approach continues until the feedback signal is above the
Signal Threshold. The parameter can be set to any value within the input range of the feedback
signal. When using a STM preamplifier with a gain of 100mV/nA, the maximum value that the
feedback current can be set to is 10 nA. A typical value for this is 100 pA. As mentioned above,
ALWAYS make sure this value is BELOW the set point knob value or the approach will
continue until the tip is fully retracted and then a crash occurs. Be careful not to set it too low or
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noise in the signal may be large enough to cross the threshold which would cause the approach
to stop prematurely. Since the software can read the value of the setpoint knob on the front panel
of the SPM100, a warning message will be produced if the threshold is set above the knob value.
For Signal test or Feedback detect modes, the Test delay is used to allow a specified amount of
time to elapse in case the head is “ringing” due to transients introduced by taking a coarse step.
The feedback signal may have large spikes above the threshold which would cause a false
engage if the signal was read before the spike decayed.
For approach types that use discrete steps, such as stepper motors, kinetic slip-stick, inchworm,
etc., Approach steps determines the number of steps between in-range tests. An in range test
should be made between a series of steps that cover between 10-30% of the range of the z piezo
motion. If you have a motor that makes very small steps, you can significantly decrease the
approach time by increasing this number since there is no need to test for tip-sample interaction
between each minuscule step. Theoretically, the approach time will scale linearly with increasing
this number. If it only tests every ten coarse steps, the approach should be ten times faster
compared to testing after every step. Similarly, Adjust Steps is equal to the number of steps that
will be made each time the ‘+’ or ‘-’ buttons in the navigation window are clicked. A typical
value would be one but larger motion can be initiated for each button press by using a larger
number. When ready to move the tip and sample far apart (for sample change, tip change, etc.),
pressing the Retract button will cause the motor to move the number of steps specified by the
Retract steps parameter.
Tip control tab
Helpful choices for tip behavior are contained in the Tip Control tab of the same window (Figure
16). Tip back in motion is the option that determines if the probe should be automatically
retracted whenever the software is about to move the probe in any direction using a coarse step.
This option should always be set to YES when used with an STM as an extra precaution when
trying to avoid tip damage. If the system is used with an AFM that can only move in the Z
direction under software control, this parameter can be safely set to NO as long as each approach
step will not cause damage to the probe if the feedback loop is slow to respond. If each step in
the z direction is large enough and rapid enough that a brittle cantilever could snap, the tip
should also be pulled back before taking the step. If motion can be taken laterally than it would
be a good idea to pull the tip back before making a large sideways step.
After an approach has finished, the tip can be left at its fully retracted position as an extra
precaution against tip damage through accidental tip-surface contact. Many times, an approach
can take a very long time and will be performed unattended. However, once the approach is done
the tip is in range and very close to the surface. Accidental contact could occur if an isolation
table is bumped or someone is unaware an experiment is taking place. By checking Tip back
after approach, when the coarse approach is finished the final part of the sequence will be to
fully retract the tip the maximum allowed z range and hold this position until it is released by the
user through the software. This can be done right away when dismissing the “approach done”
dialog or at a later time by unchecking Withdraw Tip in the Manual Control section described
later.
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Tip retract mode determines what method is used to retract the tip. TTL-Feedback will apply a
+12 V signal into the feedback circuit to simulate a large signal. This will cause the feedback
loop to fully retract the tip in an attempt to reduce the signal. TTL-Feedback is the most
commonly used control mode; however for very specific cases, Analog ramp may be better. The
feedback loop is disabled and a DAC output is applied to one of the Z modulation inputs which
will retract the tip when using this mode. This method should be used to pull the tip a controlled
distance off the surface instead of pulling it back the full z range as will occur when using TTL
Feedback. It can also be used if the TTL Feedback method has a problem retracting the tip which
can happen under certain circumstances. As the tip is retracted the output of the detector circuit
could become a large negative value. This value when summed with the +12 V signal could
cause the net sum into the feedback loop to be close to zero which could then put the SPM100
into feedback (the
input signal appears to
be equal to the
setpoint value) and
the tip would not be
retracted further. If
this occurs, the
software measures the
tip as not fully
retracted and assumes
something has failed.
An error message is
then produced which
indicates the tip
retract was not
successful.
When the tip is
retracted delays can
be introduced
between the time the
Figure 16: Screen shot of tip control
tip is pulled back and
when the coarse step
is taken as well as between the time the step is finished before the tip starts to ramp forward
again. The first one is Tip retract delay
and the second one is Tip restore delay.
Both of these can be set to zero if no
transients are introduced into a scan head
by sharp motion of the z piezo or sharp
motion of a coarse stepping mechanism.
The basic timing of a Tip Retract mode
approach is illustrated in Figure 17. The
tip begins fully extended and the
software sends a signal to the SPM 100
to retract the tip. The time it takes to
fully retract the tip, t1 is determined by
the Gain and Time Constant of the
feedback loop. When the software
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Figure 17: Basic timing of a tip retract mode approach
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detects the tip is fully retracted, it waits time t2 the Tip Retract Delay. Then the software
performs whatever is necessary to take the requested number of coarse steps (Approach Steps).
The amount of time needed here will vary widely depending on the setup for the selected
approach method (Kinetic, stepper motor, etc.) After the final step is taken, the software will
wait for a delay, t3, specified by Tip Restore Delay and then send a signal to the SPM 100 to
start ramping the tip forward to search for a feedback signal while the software monitors the Z
position. If the software senses the Z piezo has extended to the Approach Threshold value, it
sends a signal to retract the tip and the process is repeated. The amount of time it takes for the tip
to be ramped forward to the threshold, t4, and to be retracted from the threshold level, t5, will
also depend on the Gain and Time Constant settings. If the tip does not reach the threshold by
the time interval t6 then it is assumed the surface has been detected and the SPM 100 is
maintaining a constant feedback signal. The amount of time to wait is specified by Feedback
Delay.
There are two possible situations that can happen as the tip is ramped forward and their order
will be determined by the Gain and Time Constant settings. The first one is illustrated in the
figure; the second possibility is the feedback delay will occur before the threshold while the tip
is still ramping forward. This can happen if the feedback bandwidth is so small that the tip is
ramped forward very slowly. Then it will take a longer time t4 to reach the threshold and the
feedback delay t6 may elapse before the threshold is reached. In this case, XPMPro will
erroneously conclude the feedback signal has been detected and stop the approach. This will
give a ‘false engage’ and probably occur after only one step is taken. It is important to have the
feedback bandwidth large enough such that the time to reach the requested threshold t4 is shorter
than the feedback delay setting. Alternatively, the approach threshold can be set to a more
negative value so the tip does not get extended as far before XPMPro stops the extend cycle and
instructs the SPM 100 to retract the tip since it wants to take another coarse step. The final
option is to increase the feedback delay to allow sufficient time for the tip to extend to the
threshold each cycle.
Figure 18: Screen shot of secondary tab
The new Tip Retract/Signal mode uses the same general timing diagram, but instead of
monitoring the Z Feedback signal, it will look at the feedback signal itself and if the threshold is
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surpassed, then the approach is stopped. This means the Gain can be turned up quite a bit higher
and the approach/retract ramps from the feedback controller will be much faster. This leads to
faster approaches compared to conventional Tip Retract.
Advanced approach settings
The secondary tab (as shown in Figure 18) contains the settings that allow a second channel to
be monitored during approach. For some systems there are two signals that may change and if
either one shifts dramatically the approach should stop. An example is non-contact AFM where
the frequency can shift out of resonance spontaneously and the amplitude can decrease. Since
the feedback loop can only monitor one of these, this feature provides a second level of tip
protection. A second signal can be sent to an Aux channel and be checked after each step. A
‘safe’ range can be designated and if the signal goes outside these boundaries, the approach will
Figure 19: screen shot of tip ramp tab
be stopped and manual adjustments made (sweep frequency again, etc.) to return the monitored
signal to its normal condition. Select the signal to be monitored using the Channel entry box.
The output of the signal should be connected to this rear panel BNC on the SPM 100. Choose
the type of Secondary condition to test. Valid selections are Safe between limits, safe outside
limits, safe below maximum and safe above minimum or Disabled to have the approach only
depend on the primary channel (topography for tip retract and feedback detect, feedback signal
for all others). Secondary Max is the upper boundary of the secondary signal Secondary Min
is the lower boundary of the secondary signal.
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The tab that controls the open loop ramp and the z offset step mode is shown in Figure 22. Most
users will not have to set any parameters in this tab unless Open Loop Ramp is in use as the
approach mode or Analog Ramp has been selected for tip control instead of the TTL Feedback
default.
The first set of parameters are used to configure the analog ramp when TTL Feedback has not
been chosen as tip control mode. The Advance ramp speed sets the speed that the tip is moved
towards the surface. The speed should be slow enough to ensure the change in feedback signal is
detected before the tip moves far enough to create unwanted contact. This speed is usually
determined by the bandwidth of the detector circuit. The Retract ramp speed sets the speed that
the tip is retracted if no response was detected during the tip ramp. It can be set to a higher value
than approach since no monitoring is necessary and a faster approach cycle can be achieved. The
Tip retract distance determines how far to pull the tip back. If mechanical constraints require
the tip not get pulled back its maximum retraction, use this value to limit how far the tip moves
from its fully retracted position. Motion per D/A volt will depend on the vertical calibration of
the Z piezo and the BNC the DAC ramp is applied to. This value must be known relatively
accurately or tip crashes can occur.
If using the Open loop ramp approach mode to improve the speed of tip-sample approach, then
the second group of parameters are used to determine settings specific to this mode. The
Approach test ramp speed is the rate to advance the tip after each coarse step. This can be
quite high since the feedback signal will be detected very quickly with the loop open. The
maximum speed will depend on the total distance that can be traveled between the height where
a signal can be detected and a tip crash. The current depends exponentially on the distance above
the surface in STM so a reasonable value may be 1 nm. If the tip is more than 1 nm above the
surface, the current will be zero. If the height reaches zero, the tip is crashed. Therefore, the
speed cannot be greater than traveling this 1 nm distance in less than the 20 ms response of a
typical current to voltage circuit. This means the speed should be less than 1 nm/20 ms which is
~50 mm/s. For NSOM or AFM where the interactions are longer ranged (maybe 2 nm), but the
signal circuit is also usually slower (time constant of a lock-in amplifier of 3 ms), a ramp speed
of 0.33 mm/s is possible. To avoid ramping the z piezo over its full range turn ON Use distance
limits. This may be useful if there are resonances present in the scan head design which are
excited when the Z piezo is near full extension or full retraction. Also if the z piezo is modulated
to excite a cantilever, when the piezo is fully extended or contracted the excitation will not be
correct since the motion gets clipped at its endpoints. In this case, the range can be centered
about zero volts or the
piezo element's
equilibrium length. Min
and Max limits are used
to restrict the range of
motion. The Z calibration
of the piezo element must
be reasonably accurate or
the actual distance will
differ from the entered
values. The z=0 distance
is the value when the z
piezo is at its equilibrium
length.
Figure 20:Timing diagram with Z Offset Step Mode and Tip Retract
There are some scan
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heads in existence where the coarse step size cannot be made smaller than the z piezo range. In
these models, it is necessary to add a separate piezo element for z offset which must be extended
stepwise between each coarse step to “fill in” the motion taken by large coarse steps. The piezo
starts out fully contracted and if no feedback signal is detected instead of taking another coarse
step, the offset piezo is extended a fixed amount and the feedback signal checked again. This is
repeated until the offset piezo is fully extended and if there is still no signal, then a coarse step is
taken. A timing diagram if Z Offset Step Mode used with Tip Retract is shown in Figure 20. A
coarse step is taken after both piezo's are retracted and then the next coarse step is not taken until
the end of the diagram when both signals are again in the fully retracted position. Since the
offset piezo overlaps the range of the coarse step, it is safe to step forward again and be assured
the z scan element will not be fully saturated in the contracted position. Offset step mode should
be ON to utilize this offset stepwise mode and Z offset piezo should be checked when the DAC
is controlling a separate z piezo element instead the one controlled by the analog feedback loop.
However, be sure to fully understand how the head performs and what the advantages are before
turning this on as a tip crash can occur if the software is misconfigured. The Z Control DAC
selects which output DAC on the rear panel of the SPM 100 is connected to the input that
controls the offset piezo. In most cases this is the Z Offset External Control. The voltage ramp to
move the piezo is applied to this channel.
It is strongly recommended to use this mode when operating the Unisoku low temperature
microscopes. The z piezo range is quite limited in these microscopes in order to achieve high z
sensitivity and the step size usually covered by the coarse motor is larger than this z range.
Configuring approach motors
XPMPro can operate an incredibly diverse set of motors typically used on SPM heads. Some of
them require an additional TTL card (DT335) to produce pulses and some of them use the TTL
line included on the DT3016 board. The use of the PMC100 from RHK will require an
additional network connection for communication between XPMPro and the unit. Other
approach methods use one or two of the rear panel DACs to produce waveforms that will be
amplified by the high voltage amplifiers and applied to a piezo element.
Kinetic approach systems
Kinetic approach systems, also called inertial or slip-stick approach systems, utilize a sawtoothshaped (or other shaped) waveform to drive a piezo tube, shear-mode piezo stack, or walker-type
SPM's. By slowly expanding and then quickly contracting their length, they can produce
translations along the axes. Two parameter windows are used to define the necessary functions
for kinetic approach heads. After selecting the Kinetic Waveform option for approach mode,
select the Wave1 tab (as shown as Figure 21) and then enter the parameters appropriate for the
scan head in use.
If the Dual kinetic waveform is selected then the same set of parameters can be specified in the
Wave2 tab. Additionally an extra parameter in the Wave2 tab (as shown as Figure 22) allows the
user to specify if the Wave2 polarity should also be reversed when Tip Retract is chosen. These
two signals will be output on different DAC channels and can be then be summed into different
piezo segments depending on what BNC the DAC output is applied to. All of the settings for
Wave1 are present for Wave2 along with the additional parameter to introduce a phase shift
between the two signals (Offset from primary).
XPMPro allows five different waveforms to be used for different scan head systems. Choose the
correct shape for the head in use in the Waveform entry. A UHV300 STM or UHV350 AFM
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from RHK requires the Sawtooth form.
The ramp height is
determined by the
distance of the rapid
piezo "jerk" during
kinetic
approach/retraction.
For horizontal motions
(no gravity effects),
approach and retract
parameters may be
identical, while for
vertical motions
different advance and
retract parameters may
give better results due
to the effects of
gravity. The distance
to move each step
while in automatic
approach mode is set
Figure 21: Kinetics Wave 1 control tab
by the Approach
amplitude. This
setting is usually
configured to be less
than 1/8th the range of
the Z scan piezo and
certainly should not be
more than the range of
the z scan piezo. The
Retract amplitude is
used when the Retract
button in the
Navigation window is
pressed. Small steps are
usually made because
large steps can set off
resonances in the head
and make the tip crash
before the sample has
retracted far from the
sample. The number of
Figure 22: Kinetic wave2 control tab
steps to take when the
button is pressed is
entered in the Approach control tab described above. The tip and sample can be moved close
together when viewing the separation by using Tip Fast In and Tip Fast Out in the Navigation
window. This is usually done to lower the approach time when using the automatic approach
method. The tip-sample distance should be viewed using an optical microscope or video camera
to make sure the motion is stopped before contact occurs since there are no delays and no
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checking of threshold levels. The amount of travel in each step when fast motion takes place is
entered in the Fast Approach and Fast retract step size box. For horizontal motions (no
effects of gravity), approach and retract parameters may be identical, while for vertical motions
different advance and retract parameters may give better results. To take a single step in a
direction, the '+' and '-' buttons on the Navigation window should be clicked. The Adjust
amplitude sets the distance moved each time a button is pressed. This is normally used when the
scan head is already within imaging range of the surface but the user wants to make small steps
to better center the z piezo extension about its equilibrium position or to move the tip/sample
laterally to image a different part of the surface. The distance is normally small, typically no
more than 5-10% of the Z scan range. All of these motions are calibrated with respect to the
Motion per D/A volt setting. The low voltage ramp before the high voltage amplifiers is always
the ratio between the amplitude entered above and this value. If the Adjust amplitude is 100 nm
and the Motion per D/A volt is 20 nm a 5 V signal is produced just like if the Adjust
amplitude is 500 nm and the Motion per D/A volt is 100 nm. The sign is significant so if a tip
approach actually moves the tip and sample further apart, set this parameter to a negative
number if it was originally positive.
The amount of time it should take to complete one waveform cycle is set by the Period. The
waveform output can be high pass filtered in order to reduce the sharpness of some edges. This
can be necessary for certain microscope head designs that have high resonance frequencies. The
high frequency components of the waveforms can be filtered out to avoid unnecessary shaking
of the head that can lead to tip crashes and other undesirable results when approaching. This
filtering capability can provide the same functionality as the Inertial Filter knob on the front
panel of the SPM 100. The width of the filter is determined by the Filter Period. A value of zero
seconds means no filtering is applied and the waveform will be generated at the maximum
possible rate of 250 kHz when using the DT3016 board. Use the Asymmetry setting to
determine the variation from an ideal sawtooth waveform. A value of 0 means the shape is a
perfect sawtooth with an instantaneous drop to 0, while a setting of 10% means 10% of the
period is taken on the falling edge and 90% is on the rising section. The Cycle delay is used
when fast motion is taking place. With no feedback checking between steps, the ramps can be as
close together as requested. Use Cycle delay to allow some time to elapse between each coarse
step in order for transients introduced in the head by the jerking motion to decay.
The D/A output channel on the rear panel used to drive the coarse approach is chosen using the
Output channel setting. A BNC-BNC JUMPER MUST BE ATTACHED BETWEEN THIS
OUTPUT CHANNEL AND THE APPROPRIATE INPUT ON THE REAR PANEL OF THE
SPM 100.
The ramp is usually produced from 0 up to 10 volts. Since the DAC can actually range from -10
V to +10 V, larger steps are possible if needed. When Waveform polarity is set to Normal the
ramp will always be positive. If the step size requested is larger than can be produced by
ramping from 0 V to +10 V, then the user has the choice of ramping around zero symmetrically
(symmetric bipolar) or to use the full positive value and use as large of a negative voltage
needed to reach the requested step size. If the ratio between Approach amplitude and Motion
per D/A volt is 16, the DAC will ramp from -8 V to +8 V is this is set to symmetric bipolar or it
will ramp from -6 V to +10 V if bipolar allowed is chosen.
FAQ: Tip approach and retract is not working?
Solution Step:
1. make sure that scan head manipulator does not touch the scan head
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2. Check ratio between the Approach amplitude and Motion per D/A volt. Generally, the
ration is above 5.
3. Check the connection at the back panel of STM 100. If the output channel of the motor
control is set for DAC 1A, the DAC1 A should be connected to inertial input for STM
scan head and x position for AFM scan head
4. Check the DAC output with oscilloscope, the output should consistent with our design
form.
5. Check the high voltage out for the approach with attenuation to 1% probe, the output
should consistent to the DAC output. The edge of the output may be rounded.
Stepper motor
A stepper motor is a
common approach
mechanism for
ambient
microscopes. They
provide good
control when used
with a fine pitch
screw and can also
have smaller motion
due to a lever
reduction scheme.
Most motors have
four coils and if
voltage is applied in
sequence, one full
rotation of the motor
is produced. The
stepper motor
interface requires a
second board to be
Figure 23: Step motor control tab
installed in the
computer, the
DT335 model. This has multiple TTL lines which are sent to the AIM MI stepper motor driver
unit built by RHK. Each TTL line controls one of the coils in the motor. A stepper motor can
also be controlled by a customer-built stepper motor driver interface identical to the AIM MI. A
separate high current drive module is required for each coil and it must accept a TTL pulse input
to trigger the current flow through the coil. Alternatively, the stepper motor can be driven using
a standard stepper motor control chip which accepts pulse and direction TTL inputs. In this case,
the approach is configured using a different selection and the parameters are set using a different
tab discussed below.
The standard stepper motor control when interfaced to an AIM MI (or equivalent) is shown in
Figure 23. Some microscopes use a clockwise rotation for approach and others use a
counterclockwise rotation. Use CW Tip Approach to match the individual scan head to the
proper rotation for approach. To take smaller steps during any motion check the box Use half
steps which will mean there are 8 steps taken for one rotation instead of only 4. A second type of
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stepper motor is considered 2 phase because it requires two coils to be energized simultaneously
for the motor to turn properly. This motor is used in conjunction with an AIM NSOM from RHK
when connected to a Nanonics NSOM head and an AIM DI when operating a Bioscope. In this
case make sure 2 phase motor is checked.
Most stepper motors require a large current to produce rotation. When no motion is taking place
the voltages to each coil should be set to zero so no current flow is occurring. The current will
dramatically heat up the motor and subsequently the entire scan head which will cause
significant thermal drift problems. However, some scan head designs will require the coil to be
energized in order to resist motion of the motor due to gravity. If the motor holds precise
position without voltage on the coils, Coil energized at rest can remain unchecked. The pulse
width of the TTL signals will determine the speed of motion. However, do not set the pulse
width too short or no motion can occur because the coil will not be energized long enough to
turn the shaft. Change the Step time setting until the approach velocity is adequate. For most
motors a few milliseconds is sufficiently long to produce rotation. When using an AIM NSOM,
there are separate lines required to remove the current flow from the two phase motor in use. In
this case adjust the Control line 4 and Control line 5 settings until motion occurs. If an AIM MI
is in use, these can be left at Not used.
Omicron 8 channel MSCU
The eight channel MSCU features 8 output channels that can be controlled via a handset, the
serial connection, or using the rear panel SYNC connection. The recommended method is to use
the serial connection between an RS232 port on the host PC and the MSCU.
The configuration window is shown in Figure 24. The MSCU Control Mode can be set set to
TTL control, serial interface, or analog DAC control. If using the TTL option, a BNC cable
should connect TTL OUT on the DT3016 adapter box to the rear panel SYNC connector. If
using a version 8.5 SPM100, the TTL output is located on pin 15 of the rear panel Digital IO
connector. Use the handset to place the MSCU in external mode so the steps are synchronized
with the SPM100 feedback test. Refer to the MSCU manual for the steps of placing the +Z
channel to be controlled by the SYNC connection. When the approach is initiated, a message
will appear to remind the user to place the MSCU external mode in +Z channel. After the
approach is finished, the handset can be used to return the MSCU to internal mode to avoid
accidental motion of the motor or can be left in external in case additional forward steps under
computer control are desired. If backwards steps are requested, the window will appear asking to
change the MSCU external mode to the -Z channel so each TTL pulse produces reverse motion.
The preferred method is to use the serial connection. This allows any channel to be controlled
and the parameters of the motion (step time, voltage level, etc.) can all be changed via
commands. When this option is chosen enter the serial port the MSCU is connected to in COM
port entry box. The channel to be used when a coarse approach should move the tip and sample
close together is chosen using the Approach channel setting. In most cases this will be channel
3 which is the first z channel. Refer to the MSCU manual to find out which channel is connected
to the z coarse motor. If the approach moves in the wrong direction change the setting of the
Invert approach motion check box. To move any of the 8 motors interactively click on Open
XYZ Control in the main NAV window to open the control window which contains a set of
buttons for all motor channels. The number of steps moved each time one of the buttons is
clicked is set using the Steps per click parameter. To have XPMPro initialize the MSCU when
the program starts, check the MSCU connected box so serial communication is established
when XPMPro starts.
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If using the serial communication, then the voltage value for the channel can be set by the Step
voltage box. Larger steps will occur when this voltage is increased. The Step rate is used to
determine the number of steps to take per second. A larger number will mean faster motion. The
Move channel
and Move steps
can be used to
move a fixed
number of steps
immediately.
Choose the
channel and
enter a nonzero
value for the
steps and the
motor will move
that amount and
then reset the
step count back
to zero when
done.
The third
method of
controlling the
MSCU is to use
one of the two
Figure 24: Omicro MSCU control tab
DACs of the
adapter box as a
pseudo TTL output. The signal
can be changed between zero and
five volts to stimulate motion. If
using the method, the DAC is
selected by the MSCU control
channel parameter and the pulse
width of the pseudo TTL is set by
the Single step time parameter.
Omicron 3 channel microslide
controller
The original Omicron microslide
controller could operate 3 motors
using a handset. XPMPro can
simulate the operation of the
handset using the DT335 board.
An adapter box should be present
Figure 25: Omicron 3 Channel microslide controller tab
that converts the 50 pin ribbon
cable output of the computer
board into the DB15 connector that on the rear panel of the Omicron unit.
The first parameter in the Slide tab ( as show in )is Use debounce mode. This is a legacy
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parameter that should be turned off unless specifically told to activate by RHK Technology
support personnel. After starting an approach, if the observation is made that the tip is moving
backwards, change the setting of Z+ tip approach. For any microscope construction one setting
will be correct and one will be wrong. Once this is determined it should not have to be changed
again. Slider step time determines the width of the TTL pulse to produce one step. Be careful to
not set this too long or the microslide unit will interpret this as a held button on the controller
and switch into continuous motion mode. The value of this parameter needs to be wide enough
to produce a step but not so wide that multiple steps are taken. After motion stops, a relay inside
the unit is opened and there must be a short delay when switching directions in order to allow the
one relay to open and the relay tied to the second channel to close. The amount of time to wait is
set using the Direction switch time parameter.
RHK PMC100
RHK also manufactures a unit
to drive stick-slip motors
which have sufficiently high
friction that the conventional
kinetic waveform cannot
overcome. The microslide
motors from Omicron as well
as the low temperature motor
popularized by S.H. Pan are
two examples of this
construction. The motor is
driven by a parabolic
waveform which drops from
the positive voltage extreme to
the negative voltage extreme in
less than a microsecond, which
is enough to exceed the static
friction and create motion.
Figure 26: RHK PMC controller tab
The preferred way to interface
with the PMC100 is through a network connection. XPMPro can send commands over the
network to produce motion of an approach motor. It synchronizes the commands with tip
extension/contraction and subsequent testing for feedback. The tab to configure the interface to
the PMC100 is shown in Figure 26.
The IP address of the PMC100 must be entered in the configuration tab (PMC100 Motor
Controller IP) so XPMPro can communicate with it. XPMPro cannot assign an IP address to
the PMC100. The PMC100 control program should be used to assign a default IP address to the
unit. The steps needed to perform this are described in the PMC100 User's Manual. If the
PMC100 was purchased with an SPM1000 and XPMPro order, the computer will be configured
with the IP address assigned to the PMC100 at RHK. The most likely address will be somewhere
between 192.168.10.1 and 192.168.10.254.
For proper synchronization the amount of time needed for one step to be taken by the PMC100
should be entered in the Step Time box. The actual time depends on the characteristics of the
motor and the settings for the Sweep Period in the external control program. A typical time is 1
millisecond.
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Figure 27: PMC configure setting panel
To configure the output voltages or which buttons to display in the window, choose the Config
Settings button. An additional window as shown in Figure 27 will open. This can be used as a
substitute for the standalone PMC100 program delivered with the electronics when trying to
label channels or alter their output parameters. After changing the parameters, write them to the
PMC100 EEPROM by clicking the Apply button. This can also be used to change the
appearance of the window shown in Figure31 by showing more groups of buttons or fewer. As
we change the name of control channels, the corresponding label at Figure 31 will be changed
to be consisted with. Any of the motor groups checked at its title bar will appear in the control
window. Adding more buttons that will never be used during microscope operation makes the
control window itself unnecessarily large. Refer to the PMC100 manual for more details on the
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meaning and operation of the motor parameters.
The motor that should be activated when coarse approach is taking place is chosen by the
Approach Channel parameter. Usually this is the z motor in one of the three groups. If the
motion produced when Tip Approach is chosen is backwards (tip-sample separation increases)
then check the box labeled Invert Approach Motion.
XPMPro can also send a command to the PMC100 to immediately move a specified number of
steps in a given direction. The active motor is set by the Move Channel and the number of steps
to take is entered in the Move Steps entry box. When the control box is opened, the number of
steps to take each time the button is pressed is set by the Steps per Click box. To open the XYZ
button window that is analogous to the PMC100 handset click the XYZ Control button on the
NAV window below the Tip Fast In and Tip Fast Out buttons.
Inchworm(TM)/TTL
The DT335 card is required for this approach. A direction line is set and clock pulses are sent to
an external control unit like RHK's IWC100 or the ARIS 950 from Burleigh. Each clock pulse
triggers a single step so the rate of pulses will determine the velocity of the motor. The
parameters that effect this motor are displayed in Figure 28.
The pulse width is the length of time the TTL trigger pulse is HI during an approach or retract
step. If this is too short, the controller will miss it and not produce a step, as the time increases
the velocity of the motor will decrease. The fast pulse width is the length of time the TTL
trigger pulse is HI during fast in or fast out motion. If this is too short, the controller will miss it
and not produce a step, as the time increases the velocity of the motor will decrease.
Reverse direction should be changed if the motion during a computer approach is in the wrong
direction and the tip
is moving
backwards. Preset
direction can be
used to set the
direction line high
before starting a
series of pulses,
otherwise the
direction line and
first pulse will occur
simultaneously. Use
this setting if a
homebuilt TTL
pulse controller is in
use and there is a
delay between the
time the direction is
set and when
motion can start.
The standard
Figure 28: Inchworm control tab
control is done
assuming TTL HI (5
V) is the active
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value and TTL LO is at rest. If the controller in use is designed to use TTL LO as the active state
then HI enable/LO stop-hold should be checked. For most controllers this should be turned on.
If the IWC100 is in use, it can sense when a clamp/unclamp sequence is about to occur. Also, it
can take a few steps backwards after the motion is complete to reduce the probability of
“backlash” occurring in the motor. To use this feature and go back a fixed number of steps after
motion is complete, turn on Reverse reposition and enter the desired number of backwards
steps in Back off step count.
Pin 5 and 7 of DT335 board is responsible for the communication between Inchworm controller
and computer. The output of this two pins and software setting are give in .
Reverse
direction
Pre-select
direction
Hi enable/
Lo enable












Pin #
Stop
Approach
retract
5
7
5
7
5
7
5
7
5
7
5
7
5
7
5
7
x
high
x
high
x
high
x
high
x
low
x
low
x
low
x
low
high
low
low
low
high
low
low
low
high
high
low
high
high
high
low
high
low
low
high
low
low
low
high
low
low
high
high
high
low
high
high
high
Table 1: The relation between the software control and output electronic signal of inchworm controller. Here, x
represents that its status can be either high or low.  means we check this selection in the control panel.
Attocube motor
The small inertial motor made by Attocube can be operated via a serial interface to their
controller. The configuration tab for this motor is displayed in Figure 29. The serial port
connected to the drive unit is selected using the COM Port parameter. Some controllers have
multiple modules to operate more than one motor axis. The module connected to the motor used
to bring the tip and sample close together should be chosen with the Approach Axis setting. For
a single axis controller, leave the parameter set to its default of 1. If the motion during approach
is opposite of what is expected, change the setting of Invert Approach Motion so clicking
Approach will actually bring the sample and tip closer.
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Figure 29: Attocube control panel
PPC200 USB controlled piezo positioning controllers
The PPC200 replaces both the PPC100 (when
used with a UHV STM) and the PPC150 (when
used with the UHV AFM/STM). The advantage
of this equipment is eliminating the manual knob
needed to switch the direction of motion when
operating Besocke scan heads. The computer can
automatically switch the voltage dividers inside
the unit to properly apply the kinetic waveform
to the three outer legs. An additional advantage
when used with the UHV STM/AFM is the unit
is automatically switched to X mode before
Figure 30
image scanning is started so the head properly
scans the tip in an XY Cartesian plane. If a PPC200 is present and the scan head in use is either a
UHV300 or UHV 700, then choose PPC200 STM Mode for Approach System. If a UHV 350 or
UHV750 is in use, then choose PPC200 AFM Mode for the Approach System.
In order to take coarse steps in any direction the XYZ Control window should be opened as
shown in Figure 30. There are a few differences in the sequence of events when operating the
UHV STM or the UHV STM/AFM. If the STM is in use, when a direction button is pressed, the
PPC200 is switched to the correct mode, the sawtooth waveform is output from the SPM100 to
the PPC, and a step is taken. After completion, the PPC200 is switched back to ground mode.
Steps can be taken even during data acquisition without stopping the scan. The software will
temporarily pause the scan and after the step is finished the scan will start again. Also, if the step
is taken in the X or Y direction the scan frame will automatically be centered within the
maximum scan frame represented by the red box in the NAV window. A running count of steps
taken in each direction is displayed in the Steps section of the window. This can help return to a
known location if the steps are reasonably reproducible in opposite directions, which is usually
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the case. To reset any of the counters to zero, click the Reset button next to each counter.
Starting an approach
Once the motor has been configured, a coarse approach is
initiated by clicking the Approach button in the NAV
window. Depending on the type of motor in use, there may be
other buttons also available for coarse steps. One button
always present is the Retract button. Clicking this will move
the tip and sample away from each other by the number of
steps entered in the approach control window as described
previously. For a kinetic slip-stick motor, there will also be
Fast In and Fast Out buttons. Clicking this will activate the
motor until stopped by using the Stop button. To take a fixed
number of steps forward, the '+' button should be clicked and
to take the same number of steps back, use the '-' button. The
actual number of steps taken each time the button is clicked is
set by the Adjust Steps parameter described above. Both of
these buttons remain active during a scan so a step can be
taken without interrupting the image acquisition.
Figure 31: PMC 100 XYZ control
As mentioned above, the PMC100 and the Omicron MSCU
panel
have separate control panels (Figure 31 and Figure 32) with
many buttons for producing motion using the selected motor
and along the desired direction. These panels can be opened
by clicking the Open XYZ Control button in the main NAV
panel. If some other motor has been configured for approach,
that button will be grayed out.
Tip Track
This technique will be covered in more detail in a later
section of the manual. It can be used to record atomic scale
diffusion as a function of time, or try to measure the drift of
the system though the pattern matching algorithm discussed
later on is a superior method compared to the tracking
algorithm.
Figure 32: XYZ control panel
Manual control
There is a pane in the NAV window
labeled Manual Control and is shown
in Figure 33. To force the tip to be
pulled back the maximum range of the
z piezo click the Tip Retract button.
The status will change to ON and the
button will remain depressed until it is
clicked again. This can be useful for Figure 33.
diagnostics or troubleshooting purposes
as well as placing the tip far from the surface temporarily while some process takes place. Note
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the motor that brings the tip and sample together is not used. Only the z piezo is fully contracted.
To disable the analog feedback loop in the SPM100 and hold the tip at a fixed height above the
surface click the Loop Hold button. The status of that button will change to ON and the
appearance will be depressed until clicked again. Be careful to not leave the feedback loop off
for an excessive amount of time or thermal drift effects could cause unwanted tip-sample
contact. The amount of time that it is safe to leave the loop deactivated is totally determined by
the scan head characteristics and the ambient environment which will cause motion of the tip
and sample relative to each other. Either of these buttons can be pressed and scanning can be
started under these conditions, but keep in mind there will be no meaningful topography data
collected due to the lack of an active feedback loop.
To immediately output a voltage pulse
from one of the DACs (usually used to
clean a STM tip) press the Pulse 1 or
Pulse 2 buttons. These two buttons remain
active during scanning so it is quite easy
to pulse the tip during a scan and observe
the change in tip quality by comparing the
section of the image taken before the
pulse with the section of the image taken
after the pulse. It is possible to predefine
two different pulses and choose the
appropriate one for the particular effect
that is desired. The pulses are defined in
the window (Figure 34) opened using the
Pulse Setup button.
The DAC outputs can also be manually
set to a specified voltage and held there by
clicking the DAC Control button in the
pane. This window is shown in Figure 35.
To place a known output voltage on either
of the DACs available on the DT3016
board, enter the value in the box or use the
scroll buttons. The output voltage will be
changed immediately at the rate specified
by the Ramp Rate parameters. If the rates
Figure 34: Pulse setup panel
are set to zero, then the voltage will jump
to the new value at the maximum DAC output rate of the ADC board (250 kHz). Be careful
changing the output voltage since undesirable effects could occur depending on what the outputs
are connected to on the rear panel of the SPM100 or some external piece of equipment. The
value will be present on the DAC until changed again using the same entry box or if some other
routine in the software is called which effects the same DAC. The DAC cannot be switched to its
other output (A to B or B to A) unless the current output value is zero. An attempt to do this will
produce an error message. Return the value to zero before trying to use the other output. The
information boxes to the right of each control display the last function performed by this DAC.
This serves as a reminder of the connection.
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The settings are identical for each pulse and will be
discussed generically. Output channel is the rear
panel DAC to produce the voltage pulses. A BNCBNC jumper must be placed between this output
channel and the appropriate modulation input (in most
cases Bias modulation or setpoint). Image
spectroscopy pulse selects which of the two
predefined pulses should be applied when
Lithography is chosen as the Spectroscopy type wile
imaging. This allows the scan to be stopped and a
pulse applied at predefined locations within the scan
frame. Use bias volt should be checked if the voltage
levels defined for the pulse need to be adjusted to take Figure 35
into account the setting of the tunneling bias using the
front panel knob of the SPM100. This should be checked when controlling a STM. For example,
if the Bias knob on the SPM 100 is set to +1.0 Volt and the pulse height selected for the pulse is
+3.3 V, then the DAC voltage will be set to +2.3 V such that the final voltage applied to the
sample is +3.3 V. The voltage level to be applied is entered in the Lithography On volt box.
When no lithography is taking place the DAC will be set to the Lithography Off voltage. This
should normally be set to zero. The width of the applied pulse is set by the Voltage on
parameter. A time delay from when the lithography pulse is selected until the time it is actually
applied can be entered in the Delay box. To have more than one pulse applied for each click of
the button (or at each spectroscopy location within an image) increase the value of the Repeat
Count. The feedback loop can be on or off while the pulse is applied. Select the appropriate
condition using the Control loop parameter.
SPM Status
The bottom pane in the window displays the readings of all analog channels as well as the two
pulse counting channels. It also displays the current scan offset, feedback setpoint, and scan area.
These values are updated about 3 times per second when no data acquisition is taking place.
Multiple readings of each channel are acquired and averaged to reduce the variations in the
displayed values.
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To view the images as they are acquired a real-time acquisition window (RTAW) needs to be
open and configured to display the correct channel. In the main acquisition window (Figure 2)
select View/Scan Window and a submenu will appear with all channels listed that are to be
acquired during scanning (Figure 11) along with choices for forward and reverse direction unless
Record one scan direction is checked. As each channel is chosen, a new window appears with
that channel in the title bar. These can be arranged and resized to any arbitrary shape as long as
they stay within the acquisition window. Up to ten RTAW can be open within the acquisition
window at one time. An example of a RTAW is shown in Figure 36. In the title bar is the name
of the channel along with two symbols to indicate the scan direction. The triangle displays the
fast scan direction and the arrow shows the
slow scan direction. For the example shown
this is a topography channel taken in the
forward direction from the top of the scan
frame to the bottom.
RTAW toolbar
The first button in the toolbar is used to select
the data for this window. After the window has
been opened, the channel to display can be
changed from its original selection. A menu of
all channels and directions currently being
acquired is shown. This can be useful to display
the same channel and direction in more than
one window with different background
subtraction preprocessing or different amounts
of smoothing. It is also preferable to change the
displayed data this way instead of closing a
RTAW and opening a new one.
The second button sets the preprocessing to be
Figure 36: Image display panel
applied to the data before it is displayed. This
does not effect the underlying raw data that will
be saved to the file, it only effects the appearance in the RTAW. Each line of data can be filtered
before it is displayed by using the bandpass function. The icon in the toolbar updates when the
selection is changed so the user knows at a glance what processing has been applied. The
following are the explanation of different setting options.
●
Raw setting means the raw data is displayed in each line.
●
Line delta z subtract means the average value of each line is set to zero. This can help
eliminate drift and slope in the slow scan direction from the image displayed in this
window and also remove artifacts due to tip changes.
●
Line slope subtract will subtract the best fit line from each scanned line and set the
average value to zero.
●
High pass applies a high pass filter to each line scan which will eliminate DC offset as
well as any small curvature the scan may possess due to piezo nonlinearities.
●
Derivative will calculate the derivative of each line scan and display this in the RTAW.
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The third button is used to
select the smoothing applied
to the data before it is
displayed in the RTAW. The
smoothing is applied to each
line scan along the fast scan
direction only. Choices range
from no smoothing up to a 25
point smooth. As with the
processing step, the raw data
is stored in the file, the data is
smoothed for display purposes
only.
Image manipulation and
color table dialog
The small button next to the
smooth button opens the
image manipulation dialog
box which is shown in Figure
37. It is a very powerful
feature of XPMPro and allows
a user to customize the color
table to optimally match the
Figure 37: HSV tab screen shot
data representation. Also the
mapping of physical ADC
values into pixel color is determined in the HSV tab. Each color table in XPMPro is represented
by a Hue (the wavelength of the light i.e. Color), Saturation (the amount of color), and Value
(darkness). The endpoints of the color table are chosen and the rest of the table filled in using an
interpolation through the HSV color space. One of the 'X' on the circle represents the start color
and the other represents the end color. Each can be dragged to vary the Hue and Saturation.
When an appropriate location is reached the Value can be altered by dragging the slider in the
column to the right of the circle. All the way to the bottom makes the color as bright as possible
and to the top makes the color black. As each endpoint is dragged, the Value column changes in
real time as well as the actual color table shown on the right side of the window. To move
through color space in the opposite direction check the rotation radio button (Clockwise,
Anticlockwise). To enter specific values from a table known ahead of time, type the HSV
coefficients directly into the entry boxes for the start and end color. Once the table to the right
looks ideal, each color table can be named and saved by clicking the Save As New Table button
to save the table with a new name and a dialog will then popup to enter a name for the color
table.
Which color table to be used for image display is determined at the Color Mapping tab (Figure
45). Three kinds of the correspondence between the color table and data value are design in our
software: Linear, Gamma, and Double gamma. The X axis of the gray area represents the color
value which is shown below it. The Y axis represents the display values. The yellow line in the
gray area represents the corresponding between the color table and the display value. When we
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select the Gamma or double Gamma as the display mode, we can move the gray slide at the right
of this area to change the corresponding curve. The displaying color map can be changed by
select another color map at the right of the gray area, then click on the replace button.
By moving the white filled triangle under color table, we can control the range of the data that
corresponding to it. The corresponding data range is the proportional to the position of the X
axis. Another color table can be
selected to display the left out data
range by selecting the color table at
right side, clicking on add button,
then click on vacancy area. Figure
shows the effect on the double
color table. The low part of the
image have the display of double
color table. Repeat the similar
procedures will add more color
tables. At the situation of
multicolor table is used, when a
color table area is selected, click on
remove button will remove the
color table to display data values.
The color table used to view the
image when it was saved will also
be written into the SM4 file format.
On the tab, the preprocessing
selection are the same as the
section and third button. We can
view the buttons on the tools bar as
the short cut of these selections.
Though we will introduce these
definition in chapter “Analysis and
Processing”.
In the Color Map Parameters
Figure 38: Color map tab
sub-panel, the mapping function
between colors and signals is chosen. The following options are avaialable:
●
Linear means that whole range of the data would be displayed with the intensity
proportaional to the color.
●
Limited accompanied by a choice of value in the “Z exclude %” results in some
percentage of the data at the ends of the data range not being displayed are not
displayed. In this case the color table only provides a correspondence to the signal
level for the middle parts of the data.
●
Equalized mode displays the data in a nonlinear relationship between signal and color.
●
Light Shade mode makes the brightness of each pixel depend on the angle of each part
of the image surface relative to the light source. This mode is influenced by the
definition on the plot orientation tab.
●
Physical mode requires selection of 3 other parameters, Z Reference Mode, Low Z
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limit and High Z limit. Z reference defines the reference point. Software supports 7
reference modes: absolute , Center, Mean, median, mode, minimum, maximum.
The low Z limit and high Z limit defines the lower and upper range relative to the
reference point.
Figure 39: The effect of the double color table on a image
●
Logarithmic mode means the color is proportional to the logarithm of the data
●
Standard deviation mode requires specification of a parameter “Z include Sigma”. In
this mode, a statistic calculation on the data is performed and the standard
deviation and median are calculated. The displayed data are in the range of “Z
include Sigma” standard deviation value chosen above..
The next function is the autoscale. There is a short cut button to this function on the toolbar,
which is next to the image manipulation dialog button. When autoscale is checked, Color 0
will be set to the lowest ADC value and color 256 will be set to the highest ADC value. Here, we
have 3 choice of autoscale. None means that we do nothing on autoscale. Line by line means
software will autoscale the display after it obtain every line. Image by image means that the
software will autoscale after it obtain the whole image. If we use the short cut button, it means
that the autoscaling of the image will occur at the time of the mouse click. To automatically
rescale all open RTAWs, press the F5 key or use the ruler button in the toolbar of the main ACQ
window.
There are another two tabs on this window, Plot orientation and default. At the Plot
orientation tab, the light source direction can be defined when the light shade color map mode
is selected. At the default, the default scan window parameters are defined, for example, the size
of the image display window, scale bar, color scale and etc.
The last two buttons on the toolbar are for autodrift correction. We will talk discuss this function
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in the Advanced Techniques section.
The column to the right of the data section will contain a blue line which represents the range of
the ADC values in the current image. The top of the left column is the highest possible ADC
value and the bottom of the column is the lowest possible ADC value. If the blue line reaches the
top of the column, this means the signal has saturated the ADC. If the blue line reaches the
bottom of the column, this means the signal to the ADC is below its lower limit. If either of
these happen, the ADC range should be adjusted or the input signal changed to avoid ADC
saturation or underflow. In the case of the topography channel, the Z Position ADC Gain knob
on the front panel of the SPM100 should be changed. For the other channels, the ADC limits of
the DT3016 board can be adjusted (Figure 11). If the blue line is very short, the gain should be
increased because the range of data values do not cover much of the ADC so a large number of
bits are not being used, and the gain should be increased to increase sensitivity.
Navigation window
One of the most important
windows in XPMPro is the
navigation window (Figure 40)
which was briefly introduced
earlier when configuring the
coarse approach system. The
colors used to display various
parts of the window are user
configurable. Right click
anywhere in the display pane
and a menu appears with
options to change the scan size
box, the maximum scan size
box, the background of the
image area, the color of the
text in the controls, the path of
the tip when it is drawn, and
the path the tip should follow
when moved via the mouse.
When certain functions are
taking place, a text message
appears in the message box
and the color of the box
changes as a visual indication.
These colors can also be
configured from the same
menu.
The DSP scan board allows the
scan voltage to vary over any
range of values. Since the
Figure 40: Screen shot of Navigation window
output is in series with the
SPM100 front panel scan
range knob, the actual scan area is determined by both of these. For a fixed scan board DAC
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output, if the range knob is increased the scan size will increase. Also, if a front panel offset
knob is moved, the tip will physically move across the surface. The scan DACs can also provide
an offset to move the scan origin to another location on the surface and the scan would no longer
be centered about 0 V. The significant advantage to this is the complete range of scan can be
covered without concerns of digitization problem when scanning a small area. For example, if a
single 16 bit DAC is used to control the scan voltages, this provides 65536 distinct steps to cover
the entire scan area. If a large area scan head is in use with a 100 micron range, the smallest step
possible will be 100 micron/65536 or 1.5 nm so the resolution will never be better than this
figure. When using the SPM100, if higher resolution is desired it can be achieved by simply
reducing the scan range knob. Now the 65536 steps will be spread over a smaller maximum scan
range which means higher resolution scans are possible.
Moving the scan frame around the surface
This added flexibility has made the Navigation window (Figure 40) critical for locating the scan
frame and understanding how to operate the SPM100. For any given position of the front panel
Range and Offset knobs, the reachable area is displayed as a red box by default. The maximum
reachable scan area is always displayed in red letters at the top of the window. The Scan Area as
well as the X Offset and Y Offset parameters in the lower part of the panel can be changed to
move the yellow box within the region of the red box. The yellow box will represent the actual
area of the sample that will be imaged at any time. The tail of the green arrow designates the
origin of the scan, and the arrow points along the direction of the first scanned line. If the colors
are difficult to see, right-clicking
anywhere inside the sample
representation area produces a
menu which allows the colors of
the maximum scan area (red by
default), the actual scan area
(yellow by default), and the text
used in the entry boxes (yellow
by default) to be changed to suit
an particular requirement.
The scan area can be changed
using two methods. The first way
is to use the entry boxes (by
typing in numbers or using the
scroll buttons). If the Mouse
Action radio button is set to
Modify Scan Area, clicking on
the yellow box will produce
“handles” which can be dragged
to resize the scan area or relocate
it. The key pad also can be used
Figure 41
to make these changes in real
time while an image is being
scanned similar to turning the knobs when using an older electronics. Press the appropriate key
as illustrated in Figure 41. The offset shifts should be immediately visible in the RTAW as
features will be “split” and offset laterally between subsequent line scans. Lastly, the yellow box
can be shifted laterally and rotated by clicking on the arrow buttons in the window. The button
with the small square amidst the four direction buttons can be used to return the yellow box to
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the center of the red box which will set the two offset values to zero. Another option for moving
the scan area laterally is to place the mouse where the scan are should be centered and click the
right mouse button. A menu will appear and one choice is Move Scan Area Here. The scan area
box will immediately move to this new position. When the mouse action is set to Modify Scan
Area, moving the mouse cursor anywhere inside the maximum scan area (red box default color)
will also display the location of the mouse at the top of the window. This is a quick method to
record the physical coordinates of features in the window.
Anytime the scan area is changed when imaging is not taking place, the user has the option to
have the tip follow the scan frame or leave the tip stationary and not move until imaging is
started again. The second option avoids unnecessary tip motion, but the first option provides a
simple method of moving the tip position small amounts across the surface if it always remains
at a fixed position within the scan frame. To choose the first behavior )tip moves when box
moves) make sure the Tip Motion box below the Modify Scan Area is checked.
The colors for the scan area frame, maximum scan area frame, background of the navigation
area and text color of the scan area controls can all be changed to fit a user's preference. Each of
these choices is accessed by right clicking anywhere in the navigation area and selecting the
appropriate menu item.
The Load button in the Ref Image section allows the user to place any image in the scan area
window for reference purposes. When clicking on this button, the cursor will change shape and a
RTAW could be clicked or an image currently displayed in a data analysis window can be
loaded. A large image can be acquired and then placed in the Navigation window in order to
accurately reduce the scan frame to focus on a small object visible in the larger scan frame. The
image is loaded as soon as a real time display window is selected, if the image is not completed a
partial image is loaded and the rest of the image is filled in with null values. To ensure a
complete image is loaded, either stop the scan at the end of the frame and then load the image or
use the Load at End button. This selection will automatically load the selected image when it is
completed and then the next frame acquisition will start.
The horizontal and vertical lines in the NAV window represent the center of the possible tip scan
area (no piezo deflection) and are used as a reference to track how much tip motion there is
when the front panel offset knobs are turned. When an image is loaded, the black lines indicate
the center of the reference image. More than one image can be loaded at the same time and a
panoramic view provided by many images combined together can be exported from the NAV
window. Details for this function are described in the Advanced Techniques chapter.
The Zoom In and Zoom Out buttons (magnifying glass icon) are used to zoom in or zoom out
the total area covered by the map. If the user wants to move the scan frame a very precise
amount on an atomic scale to scan a specific feature, it would be best to zoom in quite a bit so
the map area is rather small and the scan frame outline will be controlled very accurately with
respect to the image loaded into the map. When zoomed in any level except maximum range, the
Navigation window is centered on the yellow box. This also means as the scan frame is shifted,
the yellow box appears stationary (since it remains centered) and the red box shifts opposite of
the direction clicked making the net effect of moving the yellow box the desired direction. If the
view is zoomed out as far as possible the view switches to centering on scanner zero. The
magnifying glass with a white appearance next to the + and – buttons can be used to
immediately return the zoom range to the maximum reachable scan area (like the scan range
knob was turned all the way to 10). This can be useful to get a “bird's eye view” of the entire
relative scan area if the red box and yellow box are both zoomed in quite a bit relative to the
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maximum scan area reachable by the head. As discussed above, if the maximum area is 100
micron and the range knob was turned to 1 such that the red box was 10 micron in size, clicking
the white magnifying glass would immediately change the Navigation window to include the
entire 100 micron range and the red box would occupy 1/10 of the space. When zoomed back to
maximum range view, clicking the white icon again will return the view to the previous zoom
level.
If the user wants to move to a different region of the surface, the Range button in the upper right
corner of the window should be clicked. The tip is retracted from the surface and it moves to the
upper right corner of the red box. As the front panel range knob is now turned, the size of the red
box will change. If the X and Y Offset knobs are moved, the location of the red box will shift.
When the knob adjustments are done, click the Range button again to return to imaging mode.
This is the only time the front panel knobs should be used to shift the imaging area when a
DSP scan board is in use. If the Range button has not been clicked and the knobs are moved,
then the Navigation window will no longer be accurate as the software will not realize the knobs
have been changed.
If a very small scan area is desired that covers less than ~ 5% of the area of the red box, the size
of the red box must be decreased using the Range knob to improve the data acquisition. The
adverse effect exists because of how the 16 bit DSP board creates the scan raster. The scan
output is +/- 10 V using a 16 bit DAC, and this signal is then amplified by the high voltage gain.
If the scan is limited to less than the 10 V limits then fewer DAC bits are used. If the scan output
from the DAC is +/- 1V, instead of having 65536 steps, there will only be 6,553 steps that can be
taken. If the scan range is reduced more so that output is only +/- 100 mV now the DSP board
can only have 655 different steps. When trying to acquire an image with a pixel density of 1,024
or larger, the DSP board can not take distinct steps for each pixel when there are only 655
possible values. All controllers that lack a separate gain stage that can reduce the scan voltages
in front of the high voltage stage will have this problem. The SPM100 solves this issue through
the use of the front panel Range knob. If the scan range requires a +/- 1V raster before the high
voltage gains stage, instead of utilizing only 6,553 bits of the DAC, it is far better to continue to
have the DAC have 65,536 steps available to scan from
+/- 10 V range and then reduce the raster voltage before
the high voltage amplifiers by using an attenuator like
the Scan Range knob. When the red box is shifted using
the front panel knobs, the yellow box moves with it as it
stays in the same location relative to the red box.
Therefore, the section of the surface to be imaged will
change if the X or Y Offset knobs in the front panel are
turned.
Data acquisition time
When acquiring images, the amount of time it requires
complete one scan line can be determined by one of
three methods. The user can decide which feels most
comfortable for a particular scan head and experiment.
The choice of selecting scan speed is made in the
Settings window shown in Figure 42. One of the three
radio buttons in the Speed section should be chosen.
The simplest to understand is the Hardware Speed
choice. In this case, the two entries in the Tip Speed
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setting of Figure 42 are grayed out and the line time is always set by the front panel knobs of the
SPM100. Each line of data (forward or reverse) will be taken in the amount of time determined
by the product of the milliseconds/line knob and the multiplier value. The slowest possible time
is 9 seconds/line. The fastest possible time is determined by the number of channels to acquire
and the pixel density. In all cases, the data acquisition rate cannot exceed the operating speed of
the DT3016 board which is 250 kHz. As the line time is decreased, the user will eventually
notice no decrease in time to acquire an image because the software automatically overrides the
setting and takes data at the minimum possible time for the given conditions. For a 128x128
image, the line time cannot be below 1 ms/line. If an attempt is made to set a value less than this
the software automatically changes it to the fastest allowable time. For a given set of conditions
(scan size, line time knob value) the actual setting of the knob will be shown in the Line Time
box and the calculated tip velocity across the surface will be shown in the Scan Speed box.
A second method is using the software Line Time value. When this is checked as shown in
Figure 44, the Line Time entry box in the Navigation window becomes a data entry window
where a value can be typed or the scroll buttons used to change the value. This is the case
illustrated in Figure 42. When the entry box is changed, the setting will immediately take effect
at the end of the scan line that is taking place when the value changes. Any value is permitted
here so this has an advantage over the knob setting in that finer control of exact line time is
possible, for example, 145 ms/line can be used instead of being limited to either 100 ms/line or
200 ms/line when using the knobs.
Both of these methods have the disadvantage that the actual tip speed across the surface changes
as the scan size is altered. To complete a scan in the same amount of time, the tip has to move
faster as the scan size is increased. The SPM100 can also operate in constant tip velocity mode
by checking the Scan Speed button. Then the Scan Speed entry box of the NAV window will
be usable and the Line Time box will be grayed out. In this case, as the scan size is changed, the
time to complete one scan line is adjusted to maintain a constant velocity over the surface. The
line time required to maintain this velocity will be displayed in the Line Time box for
informational purposes.
To acquire data over a rectangular area of the surface, the Image Aspect Ratio can be changed.
A value greater than one makes the x axis larger than the y axis. A value smaller than one makes
the x axis shorter than the y axis. Note when this is done, the pixel spacing along the x and y axis
will be different values. The Rotation Increment determines how much the scan frame should
be rotated each time the rotate button in the NAV window is clicked. The unit for the entry is
degrees. The Scan shift increment is the percentage change (relative to the current scan size) of
the X and Y Offset values for each click of the lateral shift buttons in the NAV window. For
example, if the scan size is 100 nm and the parameter is 5, one click of the left button will
change the X Offset by 5 nm. Scan shift increment is the percentage of the actual scan size that
the area should be increased/decreased for each time the increase/decrease button is clicked. If
the scan size is 100 nm and the increment is 5%, clicking the decrease button once will make the
scan size be 95 nm, another click will make the scan size be 91.25 nm.
Any time the tip has to relocate from one part of the surface to another, the speed at which it
moves can be determined two different ways. It can use the
current value of the scan speed by checking Image Speed or
a fixed value can be chosen by entering a value in the Tip
Speed box and checking that radio button. The second
choice has an advantage by avoiding the situation where the Figure 43.
scan size is rather small and the line time is slow which
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means the real tip velocity is very slow. In this case, the amount of time it can take for the tip to
move from one point to another can be long and the user might mistakenly interpret the lack of
anything happening as the software has developed a problem when this is not the case.
Once the scan size and speed have been set, scanning and data acquisition are started by pressing
the Start button on the acquisition window toolbar. Most of the parameters can be changed
during the image and the new settings will take effect at the beginning of the next scan line.
XY Graph window
If acquiring image data, the image will be formed in each RTAW on a line by line basis. Also,
each line scan can be viewed on an XY plot by opening the Image Line window by using the
menu item View/Image Line. It will appear as shown in Figure 44.. By default the first channel
turned on in the Input tab (Figure 11) will be displayed in the window. It is possible to even
Figure 44. XY graph window
display the same channel more than once in the window. In the status bar at the bottom is the
information of the current line number of the image that is displayed. This will increment from 0
up to the last line in the image (256, 512, etc. ) and then reset to 0 when the scan frame starts
over again. A separate section of the status bar will display a message that updates periodically if
the line time exceeds 2.5 seconds because the time to acquire the forward and reverse line will
trigger the behavior of all graph windows. Any time the window date update is longer then 5
seconds a message is produced to provide the user feedback that the program is busy. The width
of each status bar section can also be changed by dragging the vertical separator bar between
sections.
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Layout tab
General presentation parameters are contained in the Layout tab as shown in Figure 45. Each
graph window in the new version of XPMPro has a set of configuration panes to the right of the
graph area. To close these panes and have the data graph fill the entire window area click the x
button in the upper right corner of the window. If the panes have been closed, they can be
reopened by using the toolbar button of the window.
Any title can be typed into the entry box and the font can be changed by clicking the Set Font
button. The x and y axes can also be labeled and their fonts chosen using the Set Font next to
that box.
The colors are chosen in the next group. The grid, axes, and graph background color can each be
set individually. Click on the color rectangle to popup a standard color picker. A user can also
define his own colors using the same standard interface. Some parts of the window can be
eliminated by unchecking the correct radio button in the next group.
The axes scale controls are also in this tab. Both the x and y axis can be autoscaled or manually
adjusted to show a section of the data. When the x axis is manually changed and the y axis is set
to autoscale, the scale is adjusted to only take
into account the visible parts of data. Both axes
can also be changed to logarithmic mode instead
of linear mode. Be careful using this setting for
some types of data. Since negative values cannot
have a logarithm computed, unexpected results
may occur of the data contains negative values.
The most common application for a logarithmic
x axis is FFT data to display the relationship in
the data. The two most common applications of
logarithmic y axis display are FFT data and
spectroscopic data so measured data that varies
of a few orders of magnitude can be seen on a
single graph. Instead of manually adjusting the x
and y axis to view only a small part of the data,
the faster method is to use the magnifying glass
icon in the graph toolbar window and drawing a
box to represent the are that should fill the entire
graph window. If the x axis has been zoomed to
show only a small section of the data, the graph
can be panned to view other pieces. Either use
the scroll bar at the bottom of the window or
click the pan icon in the toolbar to grab the graph Figure 45: layout tab
and drag the viewable window.
Curves tab
The next configuration tab is shown in Figure 46. The new XY graph window can have up to
four graphs in separate panes; and each plot can display two separate channels, one on the
primary axis and one on the secondary axis. A second channel can be added to the first plot by
choosing the desired channel from the list of active channels for this acquisition from the drop
down menu under the Secondary column. It is important to understand channels to be measured
are not done here; this is done in the channel selection tab for each acquisition. Only the display
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is affected by adding or removing channels. Alternatively, a second graph can be added by
checking the Show box in the second row. When this occurs the window is split into two equally
sized graphs one below the other. In either case, the label entry box in the layout tab will now be
activated, providing the user full control over all of the text and labeling for each individual
graph pane.
Each channel can have preprocessing applied to the data before display. The action to take is
determined by the first menu under each channel name. Valid choices are Raw, Smoothed,
Derivative, Second Derivative, Integral, and
Density of States. For smoothing or derivative
modes, a Savitzky-Golay algorithm is used
for the calculation. The number of points to
use for the algorithm is determined in the
submenu for each choice. As the cursor is
scrolled over each choice, the data updates in
realtime so a reasonable choice can be made
by deciding on a nice looking graph without
smoothing away important information.
When the file is saved, the raw, unaltered data
is saved regardless of the display mode. Only
the display has the smoothing applied.
The second button under each channel
selection determines the background
subtraction to apply before displaying the
data. This display mode can be changed to
DC, AC, AC Slope, or High Pass. DC Mode
will show the data with no processing
applied. AC mode will set the average z value
for the data to zero. This will allow small
variations to be visible if a large DC offset is
present in the data. AC Slope will subtract the
best fit line for each individual linescan to
Figure 46: curve tab
remove extra slope not eliminated using the
front panel slope compensation knobs. Keep in mind the front panel slope knobs should always
be used as the first correction to optimize the dynamic range of the data. AC High Pass will
remove the DC offset from the data and also any small curvature in the data due to non linear
piezo effects. The data processing can be set for each channel independently. To change the
color of the displayed line, click the Curves button under the correct channel label and a
window as shown in Figure 47 will open. Since the imaging channel has a forward and reverse
piece of data, there are two active line display settings to choose. The two directions can have
different colors and also different line styles and thicknesses. This can be used to highlight
various features and easily distinguish between separate pieces of data when they are all very
closely spaced together in a plot. Any time there are more than one curve possible on a graph the
average can also be displayed by checking the Show check box in the first row. Note for most
imaging channels this would have little use. An exception is an image of friction loops where
displaying the average of the forward and reverse lines can have some physical meaning and
provide useful feedback in real time. Other XY plot windows that can contain many lines will
have more rows in the window. The most obvious example is point spectroscopy with multiple
curves per acquisition. Extra features related to this instance will be discussed in that section.
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While image acquisition is taking place, the tip motion can be paused by clicking the
corresponding toolbar icon. The scan can be
stopped immediately by clicking the next button
and it can be stopped at the end of the current
frame by choosing the third button in Figure 48.
When the scan is paused the tip remains at its
present location until resumed again. This can be a
good method for halting a scan partway through
the image and then performing some other
technique and when the scan resumes the upper
and lower parts of the image can form a before
and after image of the surface. If an image is
expected to be loaded into the Navigation window
for ease in locating the scan frame, it is
recommended that the Stop at End of Scan button
be pressed in order to allow the frame to finish so
a complete image is loaded. If the stop
immediately button is pressed and the scan halted
then, the image that is loaded into the Navigation
window will only be a partial frame.
The next set of buttons are used to change the scan
direction from the x axis to the y axis,
immediately scale the color mapping of each
RTAW and saving an image. These buttons are
shown in Figure 49. The scan direction change
will take effect at the start of the next scan frame if
pressed while scanning is taking place. If pressed
before the scan is started, it will take effect and be
seen on the first scan. The button will appear
Figure 47
depressed when scanning is along the y axis and
appear raised when scanning is along the x axis.
The scan can also be switched by using the F7 shortcut key. The scaling of all RTAW is like
pressing the scale button on each individual RTAW but instead resets the mapping for all
windows. This will be the mapping in effect until the button is
pressed again unless Autoscale Image in Figure 38 is checked.
In that case, at the end of each scan frame all RTAWs will be
remapped based on the range of data acquired in that scan frame.
The icon that looks like a floppy disk should be pressed if the
Figure 48
image currently being acquired should be saved to disk, when
pressed it will change appearance to indicate the presently occurring scan is going to be saved. A
user can decide on a scan by scan basis if the image is worth saving. Alternatively, Autosave
Image in Figure 10 can be activated and then it is
unnecessary to press the disk icon each time as the data will
always be saved to disk and the icon will be grayed out. If
the scan is interrupted using the Stop Immediately button,
the partial image can be saved to the disk by pressing the
save icon on the toolbar. A file will be written with the
Figure 49
acquired data and the rest of the image filled with null data.
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On the toolbar there are three separate bars that can be rearranged and stacked instead of laying
out in a linear fashion. This may be appealing to some users depending on screen resolution and
the aspect ratio of the acquisition window. Additional buttons on the toolbar can be used to open
the navigation window, open a data analysis window, open the oscilloscope,etc. All of these
buttons have equivalent menu entries so there are two choices to gain access to certain features
and windows. There are also tooltips that popup when the mouse cursor is held over each button
for a short duration.
Point spectroscopy
One of the most common measurement techniques other than standard imaging is to acquire
spectroscopic information. In most cases, the feedback loop is opened and a voltage changed
while recording other channels at each voltage step. In STM, the most common method is to
sweep the tunneling bias while recording the change in current to study the density of states near
the Fermi surface of the sample material. A second common technique is to sweep the z piezo
voltage and record the
exponential change in current
as a function of tip-sample
separation. For AFM, the most
common technique is to sweep
the z piezo voltage and record
the cantilever deflection to
gather information on the
elasticity and adhesion of the
surface.
XPMPro can acquire
spectroscopy data within an
image or without a raster scan.
There is a tremendous
advantage to taking the data
within an image because the
exact pixel of the acquired
curve is known and it can be
assured that the data was
Figure 50: Point spectroscopy setting- data input tab
acquired over a particular
feature of interest. If the data is
acquired by locating the tip
over a feature and thermal drift effects are substantial then by the time the spectroscopy data is
acquired the tip may no longer be over the feature of interest.
The tip can be located anywhere on the surface using the NAV window and spectra acquired
using the spectroscopy window start button and the data appears in the realtime spectroscopy
window. Many curves can be acquired and averaged together to reduce noise or the same
measurement repeated over and over to record the change in a signal as some other physical
phenomenon occurs that will change the nature of the recorded response. Whether acquired
during a scan at predetermined locations or acquired immediately using the realtime window, the
same setup window is used to enter all relevant parameters.
The configuration window is accessed by choosing Settings/Spectroscopy and is shown in
Figure 52. There can be four distinct sets of spectroscopy parameters stored in the parameter file.
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By default they are named Spectrum1, Spectrum2, Spectrum3, and Spectrum4 but the names can
be changed to meaningful labels. Each of the four sets has four parameter sheets to enter the
settings for this measurement.
Input tab
The Input section is used to select which channels should be acquired at each voltage step. All
channels with the check box filled in will be sampled at each voltage step. The gain of the ADC
board can be changed before reading each signal to increase resolution. If the signal will be
limited to a small range of values, the gain can be changed so all 16 bits of the board are limited
to a voltage range less than 10 V. Valid choices here are +/- 10 V, +/- 5 V, +/- 2.5 V, and +/1.25 V. To acquire photon counts as a function of voltage, turn on one or both of the photon
counting channels and enter an appropriate pulse counting time in the box next to it.
A meaningful label can be provided for all of the stored spectral routines by entering a new
name in this tab. Once the label is changed here, all other references to this mode will use this
name.
Output tab
The output sweep is configured in the tab shown in Figure 51. There are 3 modes of point
spectroscopy in XPMPro 2.0. The mode named Ramp will output a voltage from an initial value
to a final value with equal
spacing between voltage steps.
This is the conventional mode
that most users employ. A
second mode is named Discrete
and it allows a fixed number (a
minimum of one and a maximum
of ten) of voltages to be output
with arbitrary values. The steps
do not have to be equally spaced
or even in sequential order. This
can be very useful to investigate
the system response at very
specific voltages without
acquiring many voltage steps in
between that could contain data
of no interest. The mode named
Time provides the ability to
define an arbitrary waveform
output and record the system
Figure 51: Point spectroscopy setting-output tab
response at a fixed time
resolution (including the
acquisition of data when moving from voltage level to voltage level) instead of a fixed voltage
step resolution. This mode is far better suited to induce and capture dynamic phenomena.
The DAC should be chosen in the Output DAC box. For the correct result, a cable must be
connected from the selected DAC output to the desired input. For typical I-V curves, the selected
channel should be connected to one of the bias modulation inputs on the rear panel of the
SPM100. However, the flexibility of the SPM100 allows the voltage sweep to be connected to
any equipment that can accept a voltage input and change an output for the desired response
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within the system. When STM Bias Mode is checked, the DAC output is adjusted to take into
account the value of the SPM100 bias knob. Since the tunneling bias will be the sum of the knob
and any DAC voltage (when applied to a bias modulation input) the DAC limits will not be the
limits entered for the sweep. For example, if the upper limit is entered as 1.0 V and the bias knob
is set to 0.25 V, the upper limit of the actual DAC output will be 0.75 V. If this parameter is
OFF, then the values entered for the sweep limits will be the entered values and the setting of the
bias knob will be ignored.
Output units per ADC volt is used to specify the overall gain of the DAC output for the desired
effect. Whatever physical signal is being swept, the DAC voltage will be converted into a
physically meaningful value by this conversion factor. For example, if performing a forcedistance measurement, the DAC should be connected to Z Modulation #1 and the value entered
here should be the calibration of the z piezo multiplied by 13 (for a low voltage SPM100) or
21.5 (for a high voltage SPM100) since each DAC volt will be multiplied by the gain of the high
voltage amplifiers before being applied to the z piezo element. The sign of the value entered here
is significant. If any curves appear backwards or do not reflect physical reality, then change the
sign of this setting. The Spectrum units should be entered so all values related to the sweep can
be in the meaningful units. Use V for volts, m for meters, etc. such that XPMPro can apply the
correct scientific unit prefix in all cases. Never enter nm for nanometers as this will lead to
strange values such as k nm instead of micrometers. If STM Bias Mode is turned on, the units
are automatically V for volts and cannot be changed.
Ramp subsection
When Ramp spectroscopy is acquired, the specific features of the output ramp are set in the
ramp subsection. The Initial Value and Final Value are the upper and lower limits of the
sweep. When moving the z piezo, the values should be entered using the convention that z=0 is
the position of the piezo when the feedback loop is opened. The units of the values entered here
will be the meaningful units entered as Spectrum units described above. If a value is entered
that is too large given the +/- 10 V limits of the DAC output, it will be rounded to the largest
possible value. The Output increment specifies the resolution of the measurement. It cannot be
entered as a value smaller than the minimum DAC step. Points/spectrum is a calculated value
that depends on the initial and final values as well as the resolution. It is presented for
information purposes only.
Discrete subsection
When Discrete is selected the number of voltage steps to take is determined by the Output
Count. As many as ten different values can be chosen. The voltage values to use are then
entered in the ten entry boxes. All values entered that are higher than the Output Count are
ignored and do not have to be set to zero. The units displayed in this set of entry boxes will also
match the Spectrum units entered previously.
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Control tab
If the feedback loop should be off during the measurement (for I-v or F-z) then the Control
Loop should be set to Feedback Off otherwise set it to Feedback On if the loop should remain
active while the voltage is swept and the other channels recorded as a function of voltage. Many
times, the conditions of the sweep could cause inadvertent damage to the probe or sample. A
channel can be
monitored and if the
signal satisfies a
preset test condition
then appropriate
action can be taken.
To activate this
feature, Monitor
Test should be
checked. Details of
this will be
configured using the
advanced tab. The
voltage levels are
defined in the
advanced mode tab
covered below. This
mode requires the
overall data
acquisition rate to be
slowed down. When
this is activated, the
Time/Spectrum
value will change to
a slower value given
Figure 52: Point spectroscopy setting-control tab
identical conditions
with the test
disabled.
If studying semiconductors where the current rapidly falls to zero as the edges of the bandgap
are approached, often better dynamic resolution can be achieved by activating the Variable Gap
I-V Mode. In this case, the tip can be moved closer to the surface a fixed amount before the
voltage is swept, the tip can be moved closer to the surface a distance in proportion to the bias
voltage, or both conditions can be applied. The user also has the option of returning the bias to
the tunneling value and then set the z piezo back to its nominal height or setting the z piezo back
to its nominal height and then returning the bias to the tunneling value. This is selected in the
Return to Standby section which is only active if variable gap spectroscopy has been chosen. If
conventional variable gap is performed, there is a choice to make whether the tip position should
be ramped closer and then change the bias voltage to the first step of the sweep or should the
bias be ramped to the first step of the sweep and then the tip position be moved closer to the
surface.
If the experiment requires two voltages to be changed at the same time but there is no
relationship between the two and they should be set independently, then General Dual Output
is the better choice. The second voltage sweep now is not scaled with respect to the first one.
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Samples/point is used to select how many readings should be acquired at each voltage step that
are averaged together to obtain the recorded value. A higher value will improve the quality of
the data since noise in the signal will be averaged away; the maximum value is 1024. To record
multiple curves at each pixel, increase the value named Spectra to acquire.
The Sweep
rate is the rate
the voltage is
changed when
moving from
one output
value to the
next one as
shown in
Figure 55. The
output is
always
Figure 53: Time spectroscopy output
stepped using
the full 16 bit
resolution of the ADC if possible, but a smaller value here means it takes longer to go from the
current value to the next voltage step. It can be used to decrease the transient induced on the
current signal when performing I-V measurements. It can also be used to decrease the piezo
nonlinear effects due to rapidly changing the piezo length. Setup rate determines the rate to
change the voltage from zero to the first value, from the final value back to zero before turning
the feedback loop back on, and from the final value to the initial value if multiple curves are to
be acquired and alternating slow scan is off. A large value here can adversely effect the first
few points of the first curve due to undesired transients induced in the signal from a rapid change
in value. Pre-sample delay is the amount of time to wait after each voltage step is reached
before starting to acquire readings on the desired channels. It can be used to provide time for a
lock-in amplifier to reach a new equilibrium that reflects the new output value or it can be used
to provide time for transients on the current signal that are induced from a dV/dt rate of change
of the tunneling bias due to tip-sample capacitive coupling. The overall acquisition time will be
increased by an amount equal to (pre-sample delay)*(points/spectrum) since the delay will occur
at each step of the output sweep. Spectrum delay is a delay to wait after the output reaches the
initial value before reading the first point. This is only applied once per sweep at the initial
voltage step. Since the first point often requires a large voltage change it is often a good idea to
wait extra time only at the first point since the transient induced there is larger than the transient
induced moving from step to step while acquiring the data. Using the this value avoids making
the pre-sample delay large enough to accommodate the first point only which would add
unnecessary waiting time at each subsequent voltage value. Time/spectrum is provided for
information purposes. It takes into account the delays, the sweep rate, setup rate, and the
sampling time and should be used as a guide to insure the feedback loop is not turned off for too
long of a time as undesired tip-sample contact could occur. If the drift rate is relatively large, the
tip-sample separation may not be constant during the duration of the voltage sweep which is an
essential assumption when interpreting the acquired data. Try to avoid leaving the feedback loop
off for a length of time comparable to the amount of time it would take the tip and sample
separation to change a significant amount.
By default the data is acquired at the maximum rate of the DT3016 board. However, if the signal
changes very slowly over time it makes little sense to sample at a high rate. The Sampling Time
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can be used to spread out the samples so averaging of the readings makes more sense. If using a
lockin amplifier with a time constant longer than 5 microseconds it is desirable to read the data
at a rate slower than the time constant setting and this can be accomplished by altering the
Sampling Time. Keep in mind when slowing down the ADC subsystem to spread out the
readings, the DAC subsystem is also slowed down to maintain synchronization. This means for a
given sweep rate the DAC may have to produce steps larger than the LSB in order to reach the
next voltage level within the time interval defined by the sweep rate. When Alternate scan
direction is checked, the first curve is swept from the initial value to the final value and the
second curve is acquired while being swept from the final value back to the initial value. This is
the required method to obtain force distance curves in AFM and can also be used to measure the
amount of capacitive coupling between the tip and sample when the tunneling bias is swept.
When this is on, the Spectra to acquire will always be entered as an even number to obtain
pairs of curves.
To automatically have every set of curves written to the disk when using the realtime
spectroscopy window, turn on Spectrum Autosave. The files will be named according to the
autonaming convention specified in the Settings/Scan/Save tab. If autosave is off, then any set of
curves that are acquired when using the spectroscopy start button are lost unless the Save button
is pressed during the sweep (or after the sweep if it is stopped). When acquiring spectra within
an image, they are saved in the same manner that applies to saving image files, and this
parameter is ignored. Scan mode determines if the specified acquisition occurs only once and
stopped if the spectral acquisition is repeated over and over until manually stopped with the
toolbar button. This only applies when acquiring spectroscopy using the realtime spectroscopy
window and the spectroscopy start button. When acquiring spectra within an image, the
acquisition setup is only run once per pixel location.
Two acquisition modes can be used if acquiring instantaneous spectral data NOT during an
image scan. Either Single can be chosen which means the the number of curves specified by
Spectra to Acquire are measured and then the sweep stops, or Continuous can be chosen which
means the measurement is performed Spectra to Acquire number of times and then that data
either saved or thrown away and the routine started again. This will continue indefinitely until
stopped by user interaction. The two modes are analogous to image acquisition where the Scan
Count parameter in Figure 9 can be set to zero for free scanning until stopped or the specified
number of images are acquired and then the scanning automatically stops.
Advanced modes tab
In the last tab, some of the sophisticated features of the spectroscopy routine can be configured.
The parameters in the Monitor Mode and Variable Gap Mode sections will be ignored unless
specifically activated for the routine.
If the spectroscopy routine needs to be synchronized with external equipment of some sort, the
Handshaking routine can be called during each sweep. The conditions of the handshake are
configured in the handshake tab in this same window as shown in Figure 54. It will be covered
in detail later. While data is being acquired, the realtime spectroscopy window will be present on
the screen and the curves will be drawn on the graph as they are acquired. The graphics overhead
for this capability may slow down the actual acquisition rate in some cases. To make sure the
data is acquired as quickly as possible, the Suppress inline graphics updates box can be
checked. Then the curve will be drawn after the sweep has reached the final spectroscopy value
and all data for that sweep has been read.
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If a large number of curves are going to be acquired, then is usually a good idea to reestablish
feedback between curves to make sure no drift has caused the tip-sample separation to change
and all curves can be considered to be taken at the same conditions. If the drift rate is significant
over the time it takes to acquire all curves, then the separation during the first curve will not be
the same separation during the last curve and the differences in the data may be misinterpreted.
Check Stabilize
feedback to have the
loop re-enabled
between every curve
(when alternate scan
direction is off) or
every pair of curves
(when alternate scan
direction is on). The
amount of time to
enable the feedback is
set by the
Stabilization interval
setting. Make sure this
time is long enough
given the bandwidth of
the feedback loop and
the amount of drift that
takes place during a
scan. Usually 100
milliseconds is plenty
of time unless the
Figure 54: Spectroscopy setting- advance tab
feedback bandwidth is
very low. A good
check for the reliability of the spectroscopic data is to always make sure the nominal feedback
conditions are part of the sweep. Thus the feedback signal channel (if acquired) should always
be equal to the setpoint when the bias equals the tunneling bias (in I-V curves) or when z=0
(since this is the height over the surface when the feedback loop is opened). If data is acquired
that does not agree with this expectation, then the feedback loop is not active long enough and
the data has not been acquired with the tip at its nominal position while taking images.
While taking data, there are times that the voltage sweep may cause a large increase in a signal
which can adversely damage the tip and/or the sample. XPMPro can monitor any channel and
take necessary action if the channel satisfies a test condition. If monitor mode is activated in the
control tab, the test condition to satisfy is chosen in the Monitor response parameter. Valid
choices for the test condition are Safe between limits, Safe outside limits, Safe below maximum,
and Safe above minimum. The action to take when the test condition is triggered is chosen in the
Monitor response parameter. Valid choices are Stop spectrum ramp which means the current
voltage ramp is halted, the remaining points in the spectrum are set to zero and the output returns
to zero. The next curve in the set is then acquired. Stop spectrum group performs all the steps
described previously but does not attempt to acquire the next sweep if multiple curves are to be
acquired. End all acquisition performs all of the previous steps but also stops the image
acquisition if the spectroscopy was being acquired within an image. A warning message is
produced when the test condition is met if Monitor warning message is checked. The analog
channel to monitor is selected in the Monitor channel parameter. Any of the channels can be
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selected, it does not have to be one of the channels turned on in the Input/output tab. The
Monitor maximum and Monitor minimum are used to set the limits that are used in the test.
If variable gap I-V mode is activated, the parameters used to control the tip motion as the bias is
ramped are presented in the variable gap mode section. When studying semiconductors it is
often required to move the tip closer to the surface in order to increase the sensitivity of the
measurement since the tunneling current increases about an order of magnitude for every
Angstrom the tip moves closer to the surface. When performing this acquisition, the primary
DAC (the one chosen as the Output DAC in the Input/Output tab) should be connected to one of
the bias modulation inputs and the second DAC should be connected to Z modulation #2. Before
the primary ramp is started, the second DAC can be set to a non-zero voltage in order to move
the tip closer to the surface a fixed amount by setting Z offset before spectrum. This can be
combined with motion of the tip in proportion to the applied bias. To have the tip move as a
function of the bias and reach the minimum separation as the bias crosses zero, set Z change per
bias volt to a nonzero value. The optimal
value here will take some experimentation.
Too small of a value and the tip will not move
far enough as the voltage decreases and
sensitivity will not be increased enough. The
Z change per D/A volt depends on the piezo
calibration and the rear panel z modulation
input in use.
This data acquisition technique is not limited
to only variable gap I-V curves in STM.
Because of the flexibility of the SPM100 and
XPMPro, any measurement technique where
two voltages should be changed
simultaneously and the response recorded can
be achieved using general dual output mode.
The initial and final values for each ramp are
set independently. The voltage sweeps are
broken into an equal number of steps and both
voltages are changed simultaneously to the
next step and then data is acquired.
Figure 55: Z offseted I-V curve measurement
Time Spectrum tab
Many interesting phenomena can be investigated by producing an arbitrary waveform and
watching the response of the system. Instead of monotonically increasing or decreasing the
voltage sweep as in conventional spectroscopy, the output is swept from point to point in any
order and, importantly, the response signal is also measured during the sweep. With typical
spectroscopy, the response is only measured at the voltage values that correspond to predefined
increments. The exact voltage value and time when something occurs will be missed if it
happens during the voltage ramp from one step to the next. Using an arbitrary waveform and
recording the voltage at a predetermined time interval instead of voltage interval provides high
resolution (both time and voltage) measurements to capture dynamic responses. If the waveform
is programmed to “rest” at specific voltage levels for a fixed amount of time, the probability of
inducing a change can then be statistically measured through the repetition of the conditions.
An additional benefit of this implementation is realized by tying it to point spectroscopy. This
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opens the full spectrum of choices for
where to perform the measurement. It
can be acquired within an image at any
predefined points, it can be acquired at
the tips present position by parking the
tip over a specific features, and it also
can be acquired in a point to point mode
by choosing an arbitrary line, grid of
points, or randomly distributed locations.
A particularly interesting experiment
would be acquiring an image scan and
stopping over a feature and performing
this measurement, hopefully inducing a
change. When the image scan resumes
the subsequent line scans would display
the “after” picture of the surface whereas
the portion of the image leading up to the
stop would capture the “before” picture.
Figure 56:Spectroscopy setting-Time spectrum tab
Ideally the change wold be captured by
the appearance of a split feature that shows a different structure before the stop and after the
stop. This provides a very convincing argument that the structural change was indeed induced by
the Time Spectrum sweep that took place.
The parameters used to define this mode are presented in Figure 56. Most are familiar since they
are used in conventional ramp spectroscopy. An Output DAC must be selected. Be sure to have
a cable from this DAC output to the correct input so the desired voltage is controlled. If STM
Bias Mode is checked, then the cable must be connected to a rear panel Bias Modulation Input
and the output will be adjusted so the values entered produce the tip-sample bias taking into
account the value set by the bias knob on the front panel of the SPM100. If this is not checked,
then any arbitrary string can be entered for the Spectrum unit to permit entering the values in
physically meaningful units. In order to ensure proper output scaling the correct calibration also
needs to be entered in the Output Units per DAC Volt box.
The next important parameter to set is the Sampling Rate. Since the output is configured to
ramp to various values and then hold for a specified time, the response signal should be
measured at a fixed sampling rate instead of at predetermined voltage levels. The faster the
sampling rate, the better the time resolution of the experiment but also the larger the acquired
data set will be for a fixed duration of experiment. The final part of the configuration is to define
the waveform output. This is done by deciding how many distinct voltage levels are desired,
how long to rest at each level, and how quickly to move between levels. Up to ten different
voltage values can be programmed into the waveform. The waveform will start at zero volts and
move to the first voltage using the Move to Voltage1 defined time. After this, the defined level
is held for the defined time and the voltage moves to the next level over the Move Time
parameter. To picture the waveform in your mind read the first time, then the voltage level, then
the hold time, then the move time and then drop to the next line and read the next voltage level.
Repeat this method to build up the output waveform as a function of time. Once the waveform
has been defined it is a good idea to double check the total time for the experiment as calculated
by XPMPro and also to check the number of points that will be acquired. As always, be careful
to not leave the feedback loop open for an excessive amount of time if drift is a concern.
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Another nice feature is the ability to output two voltages at once. By carefully alternating the
definition of the voltage level and the hold time and move time it is possible to have two
conditions change and watch the response as one condition is held constant and the other
condition changes. If this type of experiment is desired, in effect 5 different set of conditions can
be defined if one wants to
hold an output constant
and change the other. To
activate this feature,
check the DAC Enable
button at the top of the
second column. If the
defined level from step n
to n+1 is different for
both outputs they will
ramp simultaneously. If
one voltage level is the
same for n and n+1 then
this creates a condition
where one voltage is held
constant and the other
Figure 57: Time spectrum output
ramps.
An example of a defined output waveform is presented in Figure 57. The different slopes seen
when moving from level to level are a result of varying the Move Time parameter and clearly
demonstrates the ability to acquire data while the output level is changing.
Point spectroscopy locations
Once a specific set of sweep
parameters has been entered, the
next step is to decide where to
acquire the spectroscopy data at.
Figure 58:
The simplest case is to acquire data
by performing the defined
spectroscopy sweep at the tip's current location. A second very common scenario is to scan the
surface and stop at predefined locations and perform the spectroscopy acquisition at those pixels.
To activate this feature change the spectroscopy mode tool bar (Figure 58) dropdown box from
Spec Off to whichever of the four defined spectral modes is to be executed during the scan.
XPMPro contains a vast array of options for defining the locations of the spectroscopy pixels.
These include arbitrarily defined pixels, a regular grid of pixels spread out over the entire image
(anything from 4x4 to 1024x1024) , a regularly spaced array of pixels in a defined region of the
surface, or all pixels lying along a defined line within the image.
The regularly spaced array of pixels is straightforward to understand. For example, if 64x64 is
selected and a 256x256 image is scanned then every 4 lines within the image, the tip will stop at
64 locations during that scan line and acquire the spectroscopy data. The 64 locations will be
every fourth pixel in the line. If the image pixel density was 1024x1024, then the spectroscopy
will be acquired every 16 lines. The software will not allow a spectroscopy pixel density higher
than the currently selected image pixel density.
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Choosing a regularly spaced array of points is ideal when the surface is homogeneous and the
curves will be averaged together later to
improve the signal to noise ratio of the data.
Since the curves should be equivalent
regardless of location they can all be averaged
together. Many times though it is far more
interesting to compare spectroscopy data over
a
specific feature on the surface with curves
acquired over another location. When this
type of experiment is to be performed, there
are other options that can used. The most
straightforward method is to acquire
spectroscopy at every pixel and then also
average together the ones acquired over the
feature of interest and then average together
the ones acquired over a uniform section of
the surface. The downside to this method is
taking data at every pixel can be very slow
and the image is susceptible to effects from
thermal drift in the microscope. It also
produces a large file with data that will not be
analyzed.
To optimize the data without spending
excessive amount of time acquiring curves at Figure 59: Point spectroscopy location
every pixel, the interactive choice can be used.
The specific locations should be manually defined using the NAV window and during scanning
when the tip reaches one of the predefined locations the motion is stopped and the curves are
acquired. The tool used for this is the Spec Location tab. There is a drop down list for the five
options and as soon as one is selected, the mouse action changes to Add Spec Location.
An example of how to use this feature is illustrated in Figure 59. Imagine there is an image
loaded into the window that has an interesting feature in the upper left corner. The Mouse Action
needs to be changed to Add Spec Location (if it is already not selected) and whenever the
mouse button is clicked inside the window, the location is stored and a small blue dot appears. In
the example shown many locations were defined in the upper left corner where the feature is
present and then some locations were selected within the region but away from the feature to
have a measure of the nominal spectroscopy data acquired over uniform parts of the surface.
After the data is acquired, perhaps every spec location near the feature will not be exactly over
it, but it is a simple matter to use the tools built in to XPMPro to only select the curves acquired
directly over the feature of interest. If this method is to be used, then Interactive Point should be
selected in the toolbar shown in Figure 58.
Another method to define an array of spectroscopy locations is to define a line in the NAV
window. An example of this is shown in Figure 61. A line is drawn and then the Locations
parameter is selected to choose how many segments to break the line into when defining
spectroscopy locations. Valid choices are from 2 to 256. When requesting the points to lie along
an arbitrary line within the image as shown, the Spec Location setting should be changed to
Defined Line. After defining the line, the endpoints can be dragged to change the length of the
line and the rotation buttons can be used to rotate the line. Note that if the Mouse Action is set
to Add Spec Location, the Scan Area and the Rotation angle display the length of the line and
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angle and not the image scan size until the mouse action is changed back to Modify Scan Area.
Figure 61:
Figure 60
The final choice that can be used to define an array of points is to draw a box within the scan
frame and then define a regularly spaced grid of points as spectroscopy locations, but have the
array confined to the pixels within the drawn box. An example of this is shown in Figure 60. The
box is drawn and XPMPro then displays the array of points that can fit inside the box with a
regular spacing interval. To alter the density of the spectroscopy pixels within the region, change
the Spacing parameter. This is defined as the ratio of spectroscopy pixels compared to image
pixels. The example shown is 1:8 which means every 8 pixel along a line will have a
spectroscopy pixel and they will be contained on every eighth line. This is analogous to the grid
parameter that could be defined for the entire image as defined above but in this instance they
are only contained inside this small region. The box can be resized by dragging the corners and
can be rotated using the same rotation tool like before. Similar to the behavior when drawing a
line, the Scan Size, Rotation angle, X Offset and Y Offset will display the size of the
spectroscopy location region and not the image scan size until the Mouse Action is changed
back to Modify Scan Area.
In all cases of interactive spectroscopy locations, whether defined by clicking points, drawing a
line, or defining a region the total number of locations cannot exceed 256 due to packet size
limitations for the network communication. It is important to understand this limit only applies
when defining arbitrary locations and does not apply when performing spectroscopy sweeps at
regularly spaced arrays over the entire image or performing spectroscopy at every pixel. The
total number of defined points is displayed at the top of the NAV window. When using a region,
the spacing is not allowed to be denser than what would cause the defined locations to exceed
256. If the spacing is chosen too dense, XPMPro automatically changes it to the densest value
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that keeps the points below 256. If the image pixel density is increased to the point where the
defined region will contain more than 256 points, the region is replaced with a box including a
red x to provide a visual indication that spectroscopy within a region cannot be achieved without
changing some condition.
Each of the four spectroscopy routines have their own display window. They can each be opened
by choosing the correct one from the drop down list in the main toolbar of the ACQ window.
The list will be populated by the meaningful names assigned to the routines through the Input
tab. The tabs contained in the window are the same as the Image Line window covered earlier
with the addition of a save tab to configure the saving options for spectroscopy taken outside of
an image scan and a drift correction tab explained later.
The saving options (as Figure 62 shown) are very similar to the image options from earlier. It is
Figure 62: spectroscopy window-File saving options
important to keep in mind these save options only apply to point spectroscopy data acquired
when no scanning takes place. The distinction is pretty straightforward, if the start button
contained in the spectroscopy window is pressed to commence acquisition the saving of files is
determined by the settings in the tab of that window. Spectrum Autosave will save every family
of curves when a group have been acquired. The number acquired before saving is determined
by the Spectra to Acquire parameter in the configuration window. Each group will go into a
separate SM4 file. The name can be formed automatically by choosing Save Autoname. A
dialog to edit the comment associated with the file can be opened if Comment Question is on,
otherwise the Default Comment is used. The parameter Save Drift Image will be explained in
the advanced technique section. The path to save the spectroscopy files can be defined separate
from the image data. This provides the chance to keep point spectroscopy data away from image
data if desired, but they can also be intermixed if the two directories are defined as the same
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location. A separate comment can also be entered for spectroscopy data compared to the image
data. If autonaming the files, the scheme used to form the name is determined by the root and
index entered in this tab. This provides a nice facility to name spectroscopy files with a different
name compared to image files. After any changes are made, be sure to click the Apply button so
the changes take effect.
This window has some new controls and useful features related to spectroscopy. All of the graph
windows in XPMPro have a common set of controls but also some buttons and tabs that are
specific to the window. The first unique items noticed in this window are the start/stop buttons
present in the main ACQ toolbar. If spectroscopy is to be acquired outside of an image scan, the
controls to start and stop it are the ones in this window. As discussed above, there are four
choices for the spectroscopy to be acquired. Use the dropdown list to choose what mode to
perform when the acquisition is started. The four choices are Present Position, Relative Point,
Defined Line, and Defined Region. The manner of defining these was discussed above and they
serve the same purpose. The only difference between using the spectroscopy window to acquire
the data and the image window is during this mode, the tip moves directly from point to point
and only acquires spectroscopy data. It does not scan over a square region of the surface
acquiring image data at pixel locations and also stop at these locations to acquire spectroscopy.
When multiple curves are present on the plot (Spectra to Acquire greater than 1) there is need
to select an active curve both for highlighting and to place the cursors on a specific curve. This is
done using the left and right arrow buttons. Each time one is clicked, the active curve increases
or decreases by one. The active curve number is displayed in the gray box in the middle of the
window. Additionally, when looking at stored data the status bar of the graph window will
display the location of the tip when the highlighted curve was acquired. Next to the active curve
selection buttons is a magnifying glass icon; this is used to zoom the plot. The mouse cursor
changes shape when this is active. Click and drag to form a box that determines the new visible
part of the curve. This method is usually more convenient than trying to manually adjust the x
and y axis minimal and maximal to have only part of the curve visible. After zooming to the
approximate region of interest, using the axis adjustment controls can be convenient for small
adjustments. The next icon is for the cursors. There will be two placed on the plot and they can
each be dragged around to take measurements from the plot. To see the values of the two
locations, use the Cursor tab on the right side of the window. The final icon in the group that
looks like a hand is used to pan the graph. The mouse cursor changes to a hand shape, click the
mouse to “grab” the plot and drag it in any direction to shift the field of view a desired amount.
The next control is useful to handle plots that can have a large number of curves. If Spectra to
Acquire is very large (hundreds or thousands) the plot may become confusing with so many
lines drawn on it. The active entry box (32 in the figure) can be changed to determine the
maximum number of plots displayed at one time. If this is smaller then the Spectra to Acquire
value as a new curve is acquired, the oldest curve is dropped. Keep in mind the full set of curves
will be saved in an SM4 file if the data is written to the hard drive, but they all do not have to be
visible at once. This will be very beneficial in the DAW when analyzing data at a later time. If a
measurement was taken that acquired tens of thousands of curves, it is not beneficial to try to
look at them all at the same time because the plot will be too crowded. A reasonable number can
be typed in this box so only a fixed number will be shown at any one time. For example, picking
1024 would mean the first 1024 of a file will be read and displayed. To browse another group,
the double arrow buttons can be clicked. This loads the next group (1025 to 2048) or a previous
group depending on which is clicked. The first box changes its value to reflect the curve number
of the first one being displayed. The second number reflects the number of curves plotted in the
graph.
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The final button is a toggle button used to show or hide the control tabs on the right side. If no
changes are to be made, the panel can be hidden to allow the graph to fill more of the window
size.
Once the acquisition is ready to go, use the start button to being acquiring data. To stop the
sweep right away and re-enable the feedback loop (if it is off during acquisition) use the Stop
Immediately button. To stop acquisition at the end of this group of curves (when Spectra to
Acquire has been fulfilled) use the Stop at end of Group button.
Spectrum Analyzer
A very powerful way to search for noise sources is to utilize the Fast Fourier Transform (FFT)
feature of the program. It has the same general capabilities of a spectrum analyzer as it will
sample any analog signal at a specified rate and then numerically compute the FFT when
completed. Any peaks in the spectrum indicate periodic noise in the signal and the source of this
noise should be investigated. To properly interpret the data, a few points must be kept in mind
particularly with respect to the feedback loop of the SPM100. (1) If the feedback loop is active,
the feedback signal should show no variations below the bandwidth cutoff since the loop is
supposed to maintain a constant signal by varying the z piezo signal. This means low frequency
noise will not appear in the input signal, it will only be present in the topography channel. (2)
Similarly, high frequency noise will not appear in the topography signal since the feedback loop
will ignore any signal on the input above the bandwidth cutoff and all spectra above this
frequency will be essentially flat. (3) When the feedback loop is off, then all noise sources will
usually appear in the input signal channel since the variations of the tip-sample separation will
not be corrected by the loop. This is usually the preferred method of looking for noise sources.
Measuring the input signal with the feedback loop deactivated while in range can provide the
full spectrum of noise peaks to be concerned with.
Figure 63: FFT spectroscopy window
Another important point to bear in mind is the interpretation of the spectra when out of feedback
range and when in feedback range. When out of range, the only source of noise in the spectra
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should be electrical problems due to ground loops, capacitive coupling, improper shielding, etc.
It is usually a good idea to take some spectra and change the cabling or disconnect various parts
of the circuit to see if the FFT changes. This can help narrow down where the electrical noise is
coming from and then appropriate corrective measures taken. Once the tip and sample are within
feedback range, the spectra will be a combination of electrical sources and vibrational sources.
The Noise power data display window with integrated controls is opened by clicking the FFT
icon in the main toolbar. The parameters used to setup the acquisition are contained in the Noise
Power tab as shown in Figure 63. Choose the appropriate signal to be measured using the Data
Source parameter. The Control Status determines if the feedback loop is on or off while the
data is sampled. This has a critical effect on the interpretation of the spectrum so be sure it is set
properly so the data is interpreted correctly. Spectrum delay can be used to introduce a delay
after the feedback loop is turned off before data sampling starts. If many spectra are to be
acquired and averaged together and the feedback loop is off, it may be a good idea to reestablish
feedback between pairs of curves to avoid excessive tip-sample drift. To activate this feature
change the Stabilization Interval to any non-zero value. The length of time to ensure the proper
feedback conditions have been reestablished will depend on the bandwidth of the loop which is
set by the gain of the feedback signal detector as well as the Gain and Time Constant knobs on
the front of the SPM100. If a small signal is read, the sensitivity can be increased by changing
the gain of the ADC board. The Data Range can be decreased such that all 16 bits of the
resolution are now spaced over a smaller range which will mean better sensitivity to low level
signals. Points to Acquire determines how long the acquisition will take. More points takes
longer but means a smaller frequency interval so a peak can be more accurately located. A
maximum of 8192 thousand points can now be acquired per spectrum. Spectra to acquire is
used to select how many time series of data to acquire and average together for the final FFT.
More averaging leads to less noise in the spectra and therefore a lower baseline, but takes longer
time.
To avoid anti-aliasing as much as possible the data is now always acquired at the maximum rate
(250 kHz for DT3016 channels, 2 MHz for the DT9832 USB option) and the measured
bandwidth of the signal will be half of this value. These are displayed for informational purposes
only and cannot be changed. Based on the Points to Sum setting and the bandwidth the
frequency bin size of the FFT will also be calculated and displayed. To produce finer resolution
in the acquired data, increase the Points to Sum until the displayed interval is satisfactory. The
time to acquire a single spectrum is calculated by the sampling rate and the number of points to
acquire, when this is multiplied by the total number of spectra to average together the Total
Time for acquisition will be displayed. After each spectrum is acquired, the average will be
displayed in real time which gives a great indication as the baseline noise reduces, but also can
display changes if peaks grow and shrink as changes are made that effect the noise
characteristics. If using an accelerometer to measure the vibration environment, the spectra can
be scaled to display the displacement by checking the Scale Spectrum by Angular Frequency
Squared box. Since the conversion from acceleration to displacement is achieved by dividing
the measured voltage at each frequency by the square of the angular frequency, the peaks are
then in the proper proportion of displacement instead of acceleration. Checking the
Autocorrelate box will acquire an autocorrelation spectrum instead of a frequency spectrum.
During long data acquisition, the status bar of the window will display a countdown of
remaining time until a new spectrum is acquired. This provides feedback to be sure the program
is doing something.
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The noise power window has its own save tab as shown in Figure 64. So the settings for
autonaming, save path, automatic saving, etc. can be set independently of the image data. This
provides a nice way to organize data by type in separate folders instead of a mix of images,
spectroscopy, FFT, oscilloscope traces contained in one
directory. However, if a user prefers to have all data in
one location this can still be achieved by setting all of the
save directories to the same location. After any file tab
changes have been made, be sure to click the Apply button
so
they take effect.
Note that there can only be one Noise Power spectrum
visible at any time in the acquisition window. Therefore
the curve display control is grayed out and both values are
equal to one.
Oscilloscope
Many times it is advantageous to look at signals in the
time domain instead of the frequency domain. A better
feel for the amplitude of the signal as well as quicker
viewing of the data (an FFT cannot be displayed until the
full length of data has been acquired) are two reasons
Figure 64: Saving tab of Noise power in
worth considering. XPMPro can acquire and display data
the time domain. Most of the time this will be done as a
diagnostic to check signal levels, but there are also a number of experiments where recording a
signal as a function of time either as a response to a stimulus or to have a permanent record of
the system at a specific time can be beneficial. The integrated digital oscilloscope is opened by
clicking on the scope button in the toolbar. The parameters that affect acquisition are contained
in the Oscilloscope tab.
Alternative Imaging Modes
Exciting materials properties can be investigated using special imaging techniques where
conditions are changed during the image and the effect on the images recorded. This allows a
more direct comparison of features because there is less separation in time which translates into
more confidence of no tip artifacts etc. creeping into the data.
Multiple parameter imaging (MPI)
An interesting and oftentimes beneficial imaging mode is to scan the surface at one set of
imaging conditions and then before incrementing the voltage to move the tip along the slow scan
direction, change the conditions and scan the sample again. Since the same area of the surface is
imaged multiple times, direct comparisons of features taken under different conditions can be
done. Because of unavoidable drift it is always a difficult task to try and correlate features in one
image with features in an image taken after the first one under different conditions since the two
images were not taken over precisely the same location. Of course, part of this argument is based
on the length scale of the features and the overall drift rate. If the features are large and the drift
rate relatively slow, then clearly the two features in separate images are related. The discussion
here is referring more to alignment and orientation of atomic scale features when the drift rate is
more than the feature size over the time it takes to acquire the two images.
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XPMPro allows the same area of the surface to be scanned up to four times under different
conditions. In this imaging mode, eight individual images would be acquired (four sets of
conditions, 2 scan directions) and stored in a single file. The tab to configure this mode is
contained in the Settings/Spectroscopy window and is named Multi as shown in Figure 65. To
activate this data acquisition
routine during scanning, the
Multi Volt toolbar box
(Figure 58) should be
changed from MPI Off to the
desired mode. The two most
common choices would be
either multi page or dynamic
lithography; in both cases the
same section of the surface is
scanned repeated times as
described above. In an
unusual mode, split page
mode, the scan proceeds with
a normal slow raster, but
partway through the image,
the conditions are changed so
the lower section of the
image is not acquired under
the same conditions as the top
part.
The channels recorded during Figure 65: Multi Parameter Image setting
rescan are the same ones
recorded during the first scan,
which are all channels turned on in the Settings/Scan/Input tab.
The first parameter sets the number of times to scan over the same line before incrementing
along the slow scan direction. This can be set to either 2, 3, or 4. It does not make sense to set
this parameter to one since this would be the same as conventional imaging. At the end of the
reverse line-scan the conditions are changed and before the next line is started, the SPM100
pauses for a length of time specified by the Voltage change delay. This is usually necessary in
order for the feedback loop to adjust to the new imaging conditions. The amount of time will be
dependent on the bandwidth of the feedback loop. The next four parameters are the voltage
levels to output for each scan over the surface. The first voltage is usually set to zero when not
doing STM or set to the nominal bias voltage determined by the SPM100 knob when performing
STM. Note the nominal imaging conditions are not used for any of the scans unless specifically
configured to do so. The feedback loop can also be disabled during the subsequent rescans if
desired. If performing conventional imaging of recording the channels under various conditions,
the loop would remain on during these rescans. If an advanced mode such as dynamic
lithography is performed, then the loop may need to be disabled during the rescans.
When multi-volt imaging is turned off, the output is set to the Standby voltage which in almost
all cases should be zero. Otherwise, the conventional imaging acquired after the mode has been
turned off will not be the same as before because the additional voltage applied will effect the
imaging conditions in some manner and may be unaccounted for when interpreting the images
later. If the four voltages specified are meant to change the tunneling bias during STM, then
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STM Bias Mode should be on. The actual DAC output will be adjusted such that the sum of it
and the bias knob setting is equal to the requested value If the parameter is off, then the DAC
output will be exactly equal to the value entered in the window. If zero is entered for one of the
voltage values and STM Bias Mode is on, the DAC will counteract the bias knob resulting
in a tunneling bias of zero which will cause a tip crash!
If the output voltage is affecting some other physical quantity, then the Output units can be
entered here so the values are entered, displayed, and stored in the meaningful unit instead of
volts. The conversion of the DAC output into the meaningful quantity is entered in the parameter
named Output units per D/A volt. Whenever the voltage is changed from one value to the next,
enter a speed that it should be changed using the Ramp speed parameter. This can be used to
reduce or even eliminate transients that could be induced in the system by a sudden change in
voltage level. The Output DAC is the channel that should produce the voltage. A BNC cable
must be connected from this channel to the appropriate input for the desired change in imaging
conditions to occur.
Dynamic lithography has many uses for new and exciting data acquisition and should be
carefully considered. The implementation allows a signal to be recorded by the DSP board and
as it rescans the same line over, it can output the data recorded at the corresponding pixel during
the initial trip across the surface. Additionally, with a future implementation the user will have
the opportunity to download a shape into the DSP board and have it output this as the tip scans.
As long as the number of points in the shape equals the number of pixels in the line scan, the
system will work. By recording a signal (such as topography or other channel) during the first
scan, the replay is assured of having the equal number of pixels as the rescan line.
The line can then be rescanned up to three more times with conditions changed to acquire a set
of images at the same time that show the topography and other signals acquired over the same
area of the surface to permit correlation. The changed voltage can be applied to any input
(internal or external) to achieve any desired result. It could change a magnetic field, the
tunneling bias, temperature, a z piezo to pull the tip off the surface or push the tip into the
surface, or a lockin amplifier to apply an oscillation to some signal. The loop can also be
disabled; in the case of applying the replay voltage to a z piezo this would be required.
Otherwise the loop would simply counteract the applied voltage and not change the relative tip
height above the sample.
Since the only mode currently available is to record a signal and play it back on rescans, the
correct cabling is imperative to properly interpret the result. Whatever signal is to be recorded
should be connected to DSP ADC#1 on the SPM100 rear panel. The output signal on scans 2, 3,
and 4 will appear on DSP DAC. An additional connector is also require so the DSP board
properly records the signal. The rear panel Digital IO connector needs to have pins 3 and 6
shorted together. The simplest method to achieve this is to obtain a mating connector and solder
a single wire between the two pins and then attach it to the rear panel.
If the output is to be scaled from the recorded signal, use the Output Multiplier parameter. An
example of this is when the Z Position monitor output is connected to ADC #1 to record
topography. Since this output has the front panel ADC gain applied, the recorded voltage is
larger than the actual variations. To reduce the voltage applied to the z piezo when the DSP
DAC is connected to Z Position #1 modulation input to properly replay the topographic
variations, the inverse of the ADC gain will be automatically corrected when Z monitor is
selected as the output mode. If the Z monitor is selected to be the output mode, the front
panel ADC gain knob is not allowed to adjust when the tip is scanning. Otherwise, the tip
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may be put into a situation of being crashed into the sample!!! If the other mode is selected,
the ration between DSP output signal and the record signal must be entered here.
Automatic parameter incrementing (API)
Another very powerful imaging technique is named API. Here a voltage can be changed after
every line or every
fixed number of lines as
the slow scan raster is
incremented. When the
slow scan direction is
disabled and the same
line scanned over and
over again, the image
becomes a record of the
signals as the output
voltage changes.
Assuming no lateral
drift, the same area of
the surface is scanned
repeatedly so all
variations from line to
line within the image
are due to the change
created by the voltage.
There is also an option
to have the voltage
changed after every
image instead of every Figure 66: Automatic parameters control tab
line. This creates a
series of related images
taken under slightly different conditions that can be compared. When autosave is turned on, this
allows a large sequence of images to be acquired and saved when the microscope is unattended
so complete experiments can be performed overnight when no user is present. Delays can be
introduced that will allow phenomenon to occur on their own time scale and the imaging will not
start until after the new equilibrium has been reached. An incredible array of automated
experiments are possible with this mode that can all occur with no user interaction.
The main tab to setup this measurement is the Control tab shown in Figure 66. There are three
modes possible; Input only, Output only, and Input/Output. The first one records a series of
images with a delay between each image, but does not change any voltage value during the
image or between images. The second one would only change a voltage without recording
images, and the third one is the most common method. A voltage is changed after a sequence of
events and the images recorded. All of the channels turned on in the Settings/Scan/Input tab
(Figure 11) are acquired during the scan just like conventional imaging. The difference from
conventional imaging is the possibility to alter a voltage every few lines or to setup an
experiment where a voltage is changed after each image and all acquisition continues
automatically without user intervention.
The Ramp type determines how the voltage should change. It can proceed low to high, high to
low, low to high to low, and high to low to high. The Ramp mode selects if the voltage should
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change within a single image (line by line) or after each image before the next one starts (image
by image). The limits of the voltage are entered in the next two parameters, and the Ramp
standby value specifies the voltage level the DAC is set to when no acquisition is occurring.
The Image count is used to specify how many consecutive images should be acquired for the
complete experiment when using image by image mode. In this case, the amount the voltage
changes between each image is simply the total voltage change required for the series divided by
the number of images to be acquired.
After each voltage change, an Output change delay may be needed to allow the feedback loop
to equilibrate or to provide the system time to reach a new equilibrium (if for example a
temperature was changed) before the next piece of data is imaged. The speed of the voltage
change from one value to the next is specified by Output ramp speed. The physical quantity
that is being changed can have a useful label attached to it by entering it in the text string
Output label. The DAC that should be used is selected with the Output DAC parameter. A
cable must be connected from this DAC to the correct input for the proper effect to be achieved.
The units of the output signal can be entered in the units entry box and the calibration of the
output signal is entered in the Output units per D/A volt box. This ensures the proper voltage
level is output by the DAC to create the necessary change in the phenomenon being studied. If
an offset of the driving signal is desired, it can be entered in the Offset box. If the experiment
also required handshaking with an external piece of equipment than the Handshaking box
should be checked.
If Input or Input/Output mode is selected then in addition to the channels that will be acquired at
every pixel, an independent set of channels can be read at the beginning of each line or image.
This provides a
measurement of the
system response
(temperature, pressure,
etc.) as the experiment
continues without
unnecessarily recording
them at each pixel
during an image. Any
input checked in the
Channels tab (Figure 67)
will be measured at the
beginning of each line
and stored with the
images. If a record of the
voltage output should
also be recorded then
Record Output should
also be checked, and for
a long sequence of
images taken with delays
in between, it can be
helpful to record the
time the image was
Figure 67: Channel setting for Automatic parameter incrementing
acquired. In this case,
Record time should be checked.
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Analysis and Processing
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The third major component of XPMPro is the Data Analysis window which can be opened by
clicking on the DAW button of the main launcher. Multiple DAWs can be open at the same time
to allow a large amount of data to be displayed and analyzed simultaneously. Each time a DAW
is clicked, another window will open. Each individual window will be titled Data Analysis:?
where '?' is a wildcard character representing a number.
When the window is first opened it will be blank. A Browser window can be opened by clicking
the first button in the toolbar or choosing File/Browse. The browser window will have a tree
view of all known drives on the left side and a data viewer on the right as displayed in Figure 68.
The tree view has three predefined directories that are accessible with a single click. The first
one is the Browser Path which should be set to the directory which contains all subdirectories
Figure 68
of data. For example, one organizational structure would be to create a directory named
c:\SPMDATA and under this create a series of directories labeled by user or by sample etc. Now
experimental data can be differentiated and easily categorized, but is not buried multiple levels
deep on a hard drive. The second default path is the Save Path which is the directory where data
will be saved as it is acquired. This is defined in the Settings/Scan window shown in Figure 10.
The third one is the temp path for the dataSAFE files.
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The parameters that effect the appearance of the Browser window are accessed using the tool
icon in the browser toolbar. The
window is shown in Figure 69. At
the top of the window is the
Browser Path which can be
changed by either typing in a
directory in the entry box or
clicking Select and navigating to a
particular directory. The next
option is Thumbnails in color to
determine if the images in the data
display panel on the right side of
the browser should be shown in the Figure 69
default color lookup table or in
gray scale mode. The parameter
Thumbnail mode determines what preprocessing to apply to the small images before they are
displayed. The data can be shown in Raw mode so no change is made, or Line delta z subtract so
the average value of each line of data in the fast scan direction is subtracted and then shown. A
third choice is Line slope subtract which means a first order fit is performed to each line of data
and then subtracted before the image is displayed. If High pass is selected, each line of data is
filtered to remove large features such as piezo creep or nonlinearities due to scanning a large
distance. The final choice is derivative where the local derivative is calculated along the fast
scan direction before display. Thumbnail size determines how large to make each image in the
display panel. Larger thumbnails allow more details of each image to be seen without loading it
into memory, but fewer images will be visible at any time.
When a directory is chosen in the tree view, it will be scanned for SM4 files and the names will
be listed in the panel. A thumbnail for each page of data will then be displayed on the right side
(Figure 70). To show only a particular file, click the file name and then only the data pages
contained in that file will be displayed. The small '+' symbol next to each file name can be
clicked which will show the complete listing of data pages contained in that file. An individual
page can be shown in the display by clicking the desired channel shown in the listing. Each
thumbnail is shown with the channel listed below it. To find details of a particular page, place
the mouse cursor over the image and after a short time, a window will popup that displays the
filename, channel, scan direction, and imaging conditions for that piece of data. A user can
quickly scan a large directory of data and locate the interesting images that need to be loaded
into memory for further processing and analysis.
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SM4 file format
Version 2.0 of XPMPro introduces a new file format with dramatic improvements in
capabilities. Many new features have been added to the software and new acquisition modes
have prompted a change in the format to accommodate new forms of data that can be acquired.
Speed improvements in browsing/loading data will also be seen due to the format change. It
Figure 70
should also be easier to write import utilities to call the data into third party programs for custom
analysis and processing routines not found in XPMPro. For customers upgrading from SPM32,
the old data will have to be converted to the new SM4 format in order for XPMPro to access the
data. A builtin utility has been developed for this purpose. It can be opened using Options/SM2
to SM4 Converter or clicking the toolbar button shown in Figure 71. This will
open a dialog box to locate a directory for file conversion. The existing SM2 files
are not overwritten! An SM4 file will be created and can be located in the same
directory or a separate directory. This allows parallel data analysis in that SPM32
and XPMPro will both have access to the same raw data files. The conversion
dialog box is shown in Figure 72.
The directory where the SM2 files are located is chosen via the first Select
button. When this has been done, a listing of SM2 files found in that directory
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will be seen in the lower left panel. To convert all files click the '>>' button and the listing will
appear on the right side. To convert only certain files, choose each one and click the '>' button to
have it listed on the right side. By default, the SM4 files will be placed in the same directory as
the source folder. To choose a separate folder, click the second Select button and browse to the
desired folder. When the files for conversion have been chosen and the source folder is selected,
click the Convert to SM4 button at the bottom of the window. The amount of time it will
require to convert the files depends on the speed of the computer, the amount of data in each file
and the number of files. After this step is complete, return to the browser and click on the
destination directory and a collection of thumbnails should appear in the display area of the
window. This indicates successful conversion of the old data.
Early versions of XPMPro had a different SM3
format. When upgrading to newer versions of the
software, it is recommended to run SM2 to SM4
again to properly convert the old data to the most
recent SM4 format.
For customers upgrading from a previous version
of the program, any data that is opened in version
2.0 will be automatically converted to the SM4 file
format for forward compatibility.
Loading an image into the DAW for processing
requires a simple double click on the thumbnail
image. The data page will appear in a separate
window as shown in Figure 73. In the title bar of
the window is the name of the file as well as the
displayed channel. There are also two small icons
Figure 72
to indicate the fast scan direction and slow scan
direction when the image was acquired. The small
triangle points along the fast scan direction and an elongated arrow is used to indicate the slow
scan direction (top to bottom or bottom to top). Along the bottom of the window is a status bar
that displays the scan size, the current display mode, the pixel location of the mouse along with
the z value of the data, and whether any processing has been performed on the image.
Performing a right mouse button click when the cursor is in the window displays the shortcut
menu. This can be used to change the cursor mode of the image, change the settings of how the
data is represented, change the color table of the image, and access a large variety of analysis
and image processing routines. When 2D Plot Settings is chosen, the window shown in Figure
74 appears. Use this to change the appearance of the data contained in the window. The Color
map mode designates how the physical data (height, current, force, etc.) should be mapped into
color values. The definition of the color mode have been introduced at realtime acquisition (page
52). Here we give out more explanation for the convenience of user. In the linear mode, the
display scale runs from the minimum to the maximum pixel value. If there are a few spurious
noise spikes in the image, these can use up a good portion of the dynamic range of the color
scale. A solution to this is using the limited mode where a few pixels with extreme values can be
rejected. In equalized mode, the display scale is non-linear, so that there is an approximately
equal amount of each color in the image. In light shade mode, the brightness of each pixel
depends on the angle of each part of the image surface relative to the light source. In physical, a
specified range of Z values are mapped. This is good for comparing groups of images by having
identical color scales for the entire group. In logarithmic, the color is proportional to the log of
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the Z value. This is good for Fourier power spectrum images. If standard deviation is chosen the
min and max color values are automatically determined by the distribution of the histogram
itself.
The rest of the settings in this group are only
active if the appropriate mapping mode has been
chosen. Otherwise, they are greyed out and
cannot be changed. If limited mode has been
selected then the percentage of values to
exclude from the color range is set by the Z
Exclude parameter. Adjust this to concentrate
the dynamic range of the color map to a range
where most of the data is contained. When using
the standard deviation mode, the min and max
are set to be x standard deviaitons away from
the mean value where x is specificed by Z
Include Sigma. Values of 1.5-2 will almost
unversally give a good color distribution for all
data sets. If using the physical mode, the High
Z Limit sets the ADC value that color 256
should correspond to. Similarly, Low Z Limit
sets the ADC value that color zero should
correspond to. The center of the color map is
chosen by the Z reference mode. Center sets
the midpoint of the minimum to maximum data Figure 73
values to color 128. Mean sets the average of
the data to the middle of the color scale. Median uses the ADC value at the center of the
histogram as the middle of the color range. Mode
uses the most common ADC value (the peak of the
histogram) as color 128.
If light shade is chosen for the data mode, then
Light Tilt sets the angle of elevation for the light
source. Moving this around can help emphasize
certain features like step edges and isolated tall
structures. Light Rotate sets the azimuthal angle
of the light source in a 3-D rendering. Both of
these can be changed interactively using the
mouse by choosing Ineractive Light Shading
from the popup menu of the image. However, to
display a set of images with identical light source
settings, it is easier to type the values in the entry
box so their appearance can be compared directly.
Figure 74
The data along the fast scan direction can be
processed before display. Note this does not
change the actual data, it only applies a processing function before displaying it in the window.
To smooth the data, check the Scan Smoothing box and then choose the number of points to
smooth over. The Data mode is used to perform other processing before displaying the data.
Raw will form an image of the stored data values with no processing. Line dZ subtract will set
the average value of each individual line to the same height. This helps eliminate effects due to
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piezo creep and thermal drift in the z direction. Line slope subtract calculates a best fit line to
each individual linescan and subtracts this and also sets the average value of z the same for all
lines. High pass will filter the data using a high pass filter with a bandwidth determined by high
pass range setting.
The Display rotate box can be checked if the image is to be shown rotated to the same angle as
the scan frame when acquired. This can help orient features among various images all taken at
various frame rotation angles. The images can be rotated to any arbitrary angle using the Plot
angle box directly below the check box. By default the data is displayed at the same angle it was
acquired at, but it can be rotated to other angles using this parameter.
To have a group of settings apply to all top view image plots in the future click the Set as
default button before closing the window. Any parameter can be changed on an image by image
basis, but the settings
can also be changed
universally using any
plot settings window if
this button is clicked.
Interactive
histogram
equalization
Once an image has been
saved and subsequently
opened in the DAW,
the power and control
over color maps and
adjustment of z value
vs. color increases
dramatically. When
selecting Image
Manipulation from the
menu, the image
window expands as
shown in Figure 75.
The histogram of pixel
values is displayed in
Figure 75
the upper right corner
with a color map graph
overlaid. The x axis of the histogram is the z values and the y axis on the left side is the number
of pixels. Wherever the graph has a high value, this means there are many pixels in the image
that have that particular data value. The color map graph contained inside the yellow rectangle
shows the linear mapping of z values with color. It has no relation to the histogram other than
sharing a common x axis (z value).
Underneath the histogram is the color mapping of the image. To adjust the color value of the
maximum z value grab the white slider on the right side and drag it to the left. This causes the
maximum color of the image to move to lower z values and everything above this z value will be
set uniformly to color 256. To change the z value for the minimum color, grab the black slider
on the left side and drag it to the right. All values below the minimum position will be set to
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color zero of the current CLUT.
Once there are gaps in the color mapping, additional color scales can be added. These can be
done for artistic purposes or to help emphasize certain features in the image that may be easier to
notice with sharper contrast between z values. To add a new color scale, choose alone from the
CLUT drop down box and then click the Add button. Move the cursor up to the color scale
region of the histogram graph and when its appearance changes to a '+' symbol, it can be clicked
and the new color scale fills in this gap. After adding it, a new set of sliders will be added to the
x axis region and the mapping of this CLUT to z values can be changed by dragging them. To
remove a color scale, first click the mouse cursor in the region that contains the one to remove
which turns that overlaid graph yellow to indicate it is the active one. Once this is done click the
Delete button. The CLUT disappears and all z values previously mapped to it return to the value
determined by the remaining sets of sliders.
To edit the active CLUT, use the color wheel in the lower corner in the same manner as
described previously. Move the start color and end color endpoints of the line. The image
appearance will change as the endpoints are dragged to provide immediate visual feedback of the
changes. Color lookup tables can be changed, created or deleted from this window similar to the
functions presented in the color wheel dialog from the realtime acquisition windows.
To change the color mapping from a simple linear mode to non-linear graphs, select the
correction mode from the dropdown just below the color scale. The three choices are Linear,
Gamma, and Double Gamma. Once the mode is changed to one of the gamma selections, the
overlaid graph is changed by using the vertical slider on the right side of the histogram graph.
Keep in mind the axes for the graph can be thought of as z values along the x axis and color 0 to
color 256 along the y axis.
When all of the changes are satisfactory, return the window to its normal image display state by
un-checking Image Manipulation in the popup menu. A nice feature of this window is all other
processing and analysis choices are still valid even when the window is in image manipulation
mode. This means the image can be smoothed, background subtracted, etc. and the histogram
immediately updates along with the color mapping.
Interactive light shading
When choosing this menu option the mouse cursor turns into a shining light bulb which can be
moved around to represent the orientation of the source. As the icon is moved up and down
(along the y axis of the window) the Theta angle (angle from the surface plane to the
light)changes. If the mouse is moved along the x axis, the phi angle (angle between the +x axis
and the light source) changes. At any time, the angle can be read from the status bar at the
bottom of the window. To exit this mode, use a quick double click of the mouse button to
“freeze” the light to its present position. To return to a normal top view of the data, open the
shortcut menu using a right click and un-check Interactive Light Shading on the menu.
Cursor Modes
To extract quantitative information from SPM data, there are a variety of modes that can take
simple measurements or form plots of data from the image itself. These are accessed using the
Cursor Mode submenu found in the shortcut menu. Each individual image can be in any cursor
mode at the same time. However, when an image is in one of the cursor modes, some analysis
and processing functions become disabled. This is easily recognizable by noting the menu
options become grayed out and non-selectable.
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The first cursor mode choice is Single
Point. This can be used to get a quick
reading of which pixel a particular
feature is located at and also what its
height is. As the cursor is moved over
the image the status bar at the bottom
of the window frame displays the pixel
value and the height. A fixed location
can be placed on the image by clicking
the mouse and a cross will appear
there. As the mouse is moved in the
image, the distance between the cross
and the current location is displayed in
the status bar accompanied by the
angle of the line between the two
points relative to the +x axis. The
vertical height between the two points
is also shown. The second selection
(Point/line) is used to obtain
measurements of lateral features.
When the mouse is clicked in the
image, a line appears with two
Figure 76
endpoints. Each can be moved
individually and as this is done, the
length, angle, and vertical height between the endpoints is shown in the status bar. This can be
used to place a line on the image to screen capture for a publication. An example of this feature
is shown in Figure 76.
The third choice (Section/view) can be used to extract sections of data from the image. The
window expands to include a small plot to the right of the image. When the mouse cursor is
clicked within the image, a beginning point is picked and as the line is moved around the image,
the section is displayed in realtime in the plot (Figure 78). When the appropriate cut has been
selected, pressing the Section button in the window writes the two dimensional data to a new
data page that can then be manipulated. To smooth the section as it is converted to a data page,
choose the number of points in the Image Cross Section Points entry box. Valid choices are 1
(no smoothing), 5, 9 and 25, the number determines how many nearest neighbors are involved in
the weighted average to determine the section value at that pixel. The coefficients used in each
case are displayed in Figure 77. To have a section taken from all of the data pages stored in the
same file and taken during the same scan, check the Related Page Cross Sections box. This
ensures that a section taken from the Current channel (for example) can be directly compared to
the related feature in the Topography section since the graphs all have the same endpoints. Each
channel will produce a separate XY plot, but they can be overlaid later if desired. To have a
section taken from both the forward and reverse scan directions and plotted on the same graph,
check the box labeled Dual Scan Cross Sections. A label can be added to the endpoint of the
line by typing in the label box and pressing enter. Multiple sections can be taken from the image
and each displayed with a different color and label by making the appropriate changes to the
label box and color picker before pressing the Section button to create the XY plot. To clear all
labels and section lines from the image, press the Clear button.
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When the line is drawn across the image to extract the profile, it has three handles attached. The
endpoints can be dragged to change the length while the orientation of the line does not change.
The center handle can be grabbed to move the
location of the line without changing the length or
5 point array
0
1
0
angle. A great benefit of this feature is after the
Divide by 6 to
1
2
1
Section button is clicked, the handle can be
normalize
grabbed and the line moved to another location to
0
1
0
extract a second profile. The line will be exactly
3
4
3
9 point array
parallel and the same length as the previous
Divide
by 36 to
4
8
4
section so taking sections in parallel rows of
normalize
atoms is simple.
3
4
3
1 1 2 1 1
There are three different choices for line
25 point array
orientation and this is chosen by checking the
1 3 4 3 1
Divide by 56 to line
appropriate radio button. When XY is clicked, the
2 4 8 4 2
normalize
can be drawn at any angle and any orientation.
1 3 4 3 1
When Horizontal is checked, the line is exactly
along the x axis of the image and by default
across the width of the scan. This is useful to
Figure 77
extract the data along the fast scan direction so
individual line scans can be plotted. The length can be changed by grabbing the endpoints just
like the XY line. If Vertical is checked, the line is locked to be exactly along the y axis. If the
scan took place along the y axis this is used to extract individual line scans. The horizontal and
vertical choices could also be used to extract data across the fast scan direction.
Figure 78
The next selection is angle/lattice. An image can be analyzed to obtain the unit cell dimensions
and also visualize how much drift and creep are in the image by using this selection. A small set
of axes are placed in the center of the image and the two endpoints can be moved until they are
located directly on top of a relevant crystallographic feature(Figure 79). The origin can be
moved by clicking the mouse cursor on it and dragging. Better results can be achieved by
stretching the lines as long as possible and centering them over the atomic sites. The length of
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each line and the angle between them is displayed in the information box on the right side of the
image. The small letters indicate which axis is considered the 'A' axis and which is the 'B' axis.
Piezo calibration can be checked by stretching the lines over a fixed number of lattice periods
and checking the length of the measured line presented in the entry boxes on the right side. If the
values are incorrect, the proper values (based on the known crystallography) should be entered
into the boxes for the A and B length as well as the angle between the lines. Then the Rescale
button should be pressed. An information box is presented that shows the correction factor for
the X and Y axes. These should be recorded and then the X Motion per piezo volt and Y
motion per piezo volt settings of Figure 11 changed by the same correction factor. To correct
all pages of data taken during this scan, check the Rescale all related pages box.
An easy method to check for non-linear effects such as drift and piezo hysteresis is to enter the
number of atomic periods that should be along the A axis and how many should be along the B
axis and then click the Lattice Period button. An array of dots will be placed over the image at
each calculated
lattice position
as seen in Figure
81. The color of
the dots is
chosen using the
color picker next
to the button.
Multiple periods
can be placed on
the same image
by changing the
color picker,
reorienting the
axes in another
section of the
data, entering
the correct
number of
Figure 79
spacings along
A and B, and
then clicking the Lattice Period button again. A second set of dots will be drawn and this allows
the relative registry of the two lattices to be ascertained when an overlayer is present in one
section of the image.
If spectroscopy data is acquired during a scan, the Spectra view menu item can be used to
display the image as shown in Figure 80. If the grid button is clicked, a square will be drawn at
every pixel where the feedback loop was interrupted and spectroscopy data was taken like the
example shown. An example where data was acquired at every other pixel is shown in the figure.
The cursor can be moved close to any dot and then upon selecting the spectra button a plot will
be drawn showing the family of curves taken at that location. In the example shown, the voltage
ramp was repeated 16 times at each pixel location and 16 separate curves were then acquired and
stored at each spectroscopy location.
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To gather all curves acquired over a feature or in a region of the surface, a box can be drawn on
the image using the standard
drawing tool that encloses a region
of spectroscopy locations. By
clicking the By Rect button all
curves inside this region are
plotted on a separate x-y graph
window. They can then be
averaged together for analysis.
With a plot on the screen
displaying spectroscopy data
individual curves can be removed
by using the Select lines menu
option. If, for example, one curve
in a family of 24 curves had a
single anomalous current spike, the
dataset should be eliminated so the
average is not skewed at the one
voltage value from the isolated,
large current reading. As the left
Figure 80
and right arrow toolbar buttons are
clicked, a different curve is
highlighted with a thicker line and the curve number is displayed at the bottom of the window.
Individual curves can then be hidden from view by opening the XY Line Format dialog box,
clicking on the channel button to open the line draw dialog box. This is where
colors can be changed and line thicknesses can be specified. To hide a curve,
remove the check mark from the box in the far left column. Curves that were
hidden can be retrieved to be displayed again by placing a check mark in the
Figure 81
box. To display the average of only the selected curves, pick selected ave +
data or selected ave only in the Display Settings dialog.
A group of spectroscopy curves from different images can be averaged together by combining
all of the I-V curves into one plot. This is done using the Add plot function in the direct access
menu. All other graphs should be shown on the screen and then clicking on each window will
draw all plots from the selected window in the current graph. After the different graphs have
been combined, all normal functions available for a single plot window are available (show/hide
curves, average curves, write to file, etc.).
Data Analysis
Many different analysis routines exist in XPMPro. These can be conveniently accessed using the
Analyze submenu in the shortcut menu available from any image. Most of the routines can be
performed on an entire image or a portion of an image. The concept of region selection is
important to introduce at this point in time. To explicitly define a region within an image, click
the Draw Rectangular Region icon in the toolbar (left side of Figure 81) and then draw a box in
the image. Small black squares will appear on the box as shown in Figure 82 which can be
dragged to increase/decrease the size and location of the box within the image. When any routine
is selected it will only be calculated using the data inside the defined region. To erase the box
from the data and return to analyzing the entire image, click the Erase All Regions icon shown
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on the right side of Figure 81.
Selecting Image Histogram will create a plot that presents the distribution of heights in an
image. This can be helpful for visualizing the distribution of terrace sizes or the homogeneity of
an array of features in an image. It also allows the direct calculation of coverage in an image
because features such as adsorbates, etc. will have a
characteristic height and produce a local peak in the
distribution. The relative percentage of this peak
compared to the total pixel density would provide
an overall coverage in an image. When the
histogram is selected, a window (Figure 83)will
appear to choose the bin size of the calculation. By
default it is set to the least significant bit (with the
appropriate units depending on the channel) when
the data was acquired which is determined by the
gain on the ADC board and the z position ADC
gain knob on the front panel of the SPM100 in the
case of topography data. If the data can be grouped
more coarsely than this, increasing the binning can
be done using the stroller buttons or typing a value
directly. When a number is entered directly it will
be rounded to the closest multiple of the resolution
for that measurement. Press the Calculate button to Figure 82
create a histogram plot in a separate window. This
can remain on the screen and the binning changed to compare the appearance using a variety of
bin sizes.
An example of a histogram plot is presented in Figure 84.
Note the histogram exhibits a definite quantization in the
z heights due to the image having two large terraces
which leads to a clustering of z values into the range
occupied by the two terraces. Since the page has been
properly background subtracted to produce very flat
regions, almost all of the data in a single terrace is at the
same z value. This produces sharp peaks in the histogram Figure 83
because there is a large percentage of the pixels at the
values given by the vertical separation of the atomic height steps and very few pixels at other
heights. This illustrates an important point about the histograms: many times to extract the
desired data the background subtraction must be able to produce a page with almost no residual
slope or the histogram will show smeared out features because of the gradual change in z values
across the slope. The figure also contains a second plot based on a bin size a factor of 100 higher
than the bin for the first plot. The overall shape is similar but the curve itself has fewer points to
plot so each segment is more noticeable. Also, note carefully the y axis label in the first one
compared to the second one. The units in the first graph are m% which means millipercentage.
There are tens of thousands of pixels in the image and the bit noise is so low that any given bin
when taken at LSB resolution has very few pixels with that exact value. This leads to a small
population density in any individual bin and when dividing by the huge number of pixels the
relative population of each bin is far below 0.1% so XPMPro displays the y axis in milli-percent.
In the second graph the bin size has been increased to such an extent, many of the values have a
large number of pixels at that z value and therefore the y axis units are percent.
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Averaging together individual lines of an image can reduce noise and help some features be
Figure 84
easier to recognize. The menu option named Image X Average and Image Y average will
perform the calculation either along the x axis or the y axis. If no region is defined, the
calculation is done on the entire image; if a region
has been selected then the calculation is done on the
data inside the defined box. A window (Figure
85)will open that determines what type of averaging
to perform. For Local Maxima and Local Minima
each pixel of the line scan is searched on each side
the number of pixels specified in the Local
Min/Max Range entry box and the point is only
considered the minimum/maximum if no point on
either side is lower/higher than it. There is little
Figure 85
point to specifying the value 1 as this will consider
every point a local minimum/maximum. If a value of three is entered, then the lowest/highest
point within seven pixels (3 on the right and 3 on the left) will be found and averaged with all
other lowest/highest points on successive lines to create one plot where the lowest points along
each line are averaged together to reduce noise fluctuations. This is very useful to see the
average amount of minimum or maximum friction that builds up if stick/slip motion is occurring
during a contact AFM scan. An example is illustrated in Figure 86 where three consecutive line
scans from a simulated friction image have been offset for clarity. With a wide enough range, the
peaks in the lines will be correctly correlated as
shown and then averaged together to find the
average value that the maximum friction force
reached. If All Points is chosen for the mode, then
the value at each pixel along the x or y axis is
averaged for all lines in the image to get the
average value for that pixel in the image. This can
prove useful to help see atomic resolution features
if there is still quite a bit of noise in each line scan. Figure 86
The averaging will help reduce the random noise
fluctuations and make the atomic-scale, repeatable features stand out. Note this is only useful if
the features of interest lie exactly along the y-axis in the image. Otherwise, the averaging will
either smear them out laterally or average them away completely. If the slow scan has been
disabled then it can be a very powerful technique for getting a better signal to noise ratio for
some quantitative values to present in a single XY plot.
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Another quantitative tool is accessed by the Image Statistics menu item. The overall slope of
the region (or entire image) is calculated along with the maximum and minimum z values.
Additional information involving the deviation of the z values and the effective volume above a
standard plane is also shown. An example of the statistics box produced from the subregion
defined in Figure 82 is shown in Figure 87. The routine subtracts a plane from the whole image,
then in the selected subregion, it finds min,
max and mean, also the plane slope and the
RMS error RELATIVE TO the fit plane.
This is the "rms error" number. The
"average and standard dev" numbers are
absolute rms of the data (ie unrelated to the
fit plane). The "standard deviation" can be
considered the "typical" RMS roughness
that other SPM software provides. This
value will give a non-zero RMS for an
absolutely flat, but sloped, plane which can
be considered misleading. For a flat but
Figure 87
tilted surface, the "rms error" is closer to the
"real" roughness because it is relative to the
first order plane which should not be considered a factor in roughness. For a non-flat or stepped
surface, the fit plane parameters are not really useful. A user
can be convinced of this through a simple test, calculate the
image statistics of an image with substantial slope. Now
perform a plane subtraction to the image and again calculate
the image statistics. This time, the rms error and the standard
deviation will be the same value and also be the same value
as the standard deviation from the previous image before the
plane fit occurred. Since the standard deviation is based on
the data after a plane fit has been performed, if the plane fit Figure 88
was done before e the statistics calculated, the plane
subtraction done while calculating the statistics has no effect on the answer. Be careful of
quoting an rms error value because the figure could be dominated by background slope effects
and have no relationship to the relative corrugation of the data.
A two dimensional Fast Fourier Transform can be calculated from any data page by choosing
Image 2D FFT. It will always be calculated on the entire
image even if a region has been defined by the box. There are
two choices that can be made when this menu item is selected
as shown in Figure 88. The first one will usually be kept on
logarithmic because this provides the best dynamic range of
peaks visible in the result, but the spectrum can be shown in
one of the other topview plot modes if desired. The Power
Figure 89
display min feature size can be adjusted to not show any
data smaller than the specified size. Since the FFT has long
wavelength peaks in the center of the map and short wavelength peaks at the edge, the value
provides the cutoff distance that the edge of the spectrum map will not go past since no
meaningful data will be contained at those frequencies anyway. It is a simple method to “zoom
in” on the peaks of interest and not display the result for the data near the outer edges of the 2D
FFT. The FFT provides a spatial power spectrum of the data and therefore provides information
on the spacing of the lattice in atomic resolution images. Additionally this can show the presence
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of any non-linear effects in the data since the orientation of the peaks in the 2D FFT will also
reflect the shape of the unit cell. For example, an image of highly oriented pyrolytic graphite
(HOPG) has a hexagonal unit cell and the FFT peaks should also be hexagonal in shape and
centered around zero with no distortion. The unit cell of a 2x1 reconstruction of Si(001) will be
rectangular so the FFT of this data would also show a rectangular array of peaks.
The local slope of the surface in the x or y direction can be calculated using Image X slope and
Image Y Slope and Image Gradient. The calculation is
also performed on the entire image regardless of whether
a smaller region has been selected or not. A one
dimensional local Savitzky-Golay algorithm is used for
the calculation. The pixel width to use when calculating
the local slope is determined by Image Slope Points
entered in the window shown in Figure 89. The
Calculate button can be pressed and the result will be
displayed in a separate window. To compare results
using different widths, change the value and press
calculate again and both results will be visible in
separate windows. This provides a simple way to
understand the effect of various pixel widths on the
result. The wider the pixel value, the smoother the
Figure 90
derivative will be, but a loss in detail will also take
place. The derivative of each line of data in the correct
direction is calculated and an image formed by combining the differentiated lines. When Image
Gradient is chosen, the slope in the X and Y directions are both calculated on a pixel by pixel
basis and the image is a representation of the two slopes combined. This is particularly useful in
AFM friction measurements to see the boundary
between regions of local variations in the
frictional coefficient.
If an image contains a repeatable pattern of some
sort, Image Correlate can be used to find all the
locations of the repeatable pattern as well as the
average appearance of the pattern. Use the Define
Regions icon to draw a box around the feature to
use as the "kernel". A good illustration to explain
the concept is the image shown in Figure 90. A
small region is picked that has an isolated
adsorbate on the surface and then the calculation
Figure 91
takes place. The routine will move this sub-region
over the image and measure how well it "fits". A new, interactive AutoCorrelate image page is
created which shows the degree of fit across the image (Figure 91). All of the locations of the
adsorbate are marked with a small blue circle and cross. This location is determined by any place
where the correlation was above 40% since this was defined as the Threshold value in the
window. If there are obvious places where a cross is located and should not be there, increase the
threshold of the cutoff and recalculate. If the fit falls below the cutoff value, then the dot will be
removed from the plot as the kernel is no longer considered to be at that location. This can be
used to provide a visual overview of all adsorbate sites. Theses can be exported in pixel
coordinates to be used for external calculations such as mean spacing, distribution, coverage, etc.
Note on the lower terrace the atomic rows are visible in the correlation function. This is because
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the area enclosed by the box also encloses a few atomic sites and as the box is shifted over the
image, when it moves one atomic spacing, the correlation will increase because of the better
overlap of the atomic sites in the image and the atomic sites within the kernel. Also, the
correlation is very low at the step edges because the overlap is poor since the adsorbate is on a
terrace and the pixels at a step edge show large variations in z. This is responsible for the dark
regions running along each step edge in the image. To view the correlation map without the
crosses, click the Clear button.
Also, all the regions with a correlation above a threshold (set in the correlation window) are
averaged together to produce an optimized kernel (Figure 92). Since all of the features that
matched the defined kernel are averaged together signal to noise ratio is greatly reduced and a
more idealized or averaged appearance of the interesting feature can be seen. To manually
remove one of the locations from the averaging
calculation, make sure the Remove Points radio
button is checked and click on the cross to
remove that location.
A cross distribution of any two images of the
same size can be calculated using the 2D
Histogram menu item. When chosen, the cursor
changes shape and two images should be
selected. The Z values of the first data page are
plotted along the X axis, and the Z values of the
second image are plotted along the Y axis. The Z
values of the result correspond to the number of
pixels having the corresponding pair of Z values
in the original images. All the points in the 2D
correlation of an image with itself will lie on the
diagonal, indicating perfect correlation. This tool
is most useful for correlating contrast between
multiple images of the same area, such as
friction and topography, or tunnel current and
Figure 92
conductance, or left and right scans.
Two images can be subtracted to look for differences between them using the Image Scaled
Sum selection. After choosing the two images, a window will appear where the relative scaling
between the two images, c, is entered. Then each pixel of the first image is added to the same
pixel of the second image using the formula ZimageA + c*ZimageB The two images must have the
same units (both topography, both current, etc.) as well as identical pixel resolution (you cannot
subtract a 256x256 image from a 512x512 image). This can be very useful to notice the change
in the surface as a function of time or to subtract the left and right scans from each other when
acquiring friction data to visualize the different cantilever response in going from region 1 to
region 2 instead of region 2 to region 1. To subtract two images, use a value of (-1) for the
coefficient.
Image Processing
When any image processing procedure is selected, the type of window that appears depends on
the process that is chosen. For a calculation that has no user selectable parameters, the dialog
box will describe the calculation and contain two buttons. The first one will Cancel the
calculation and leave the original data intact. The second one will Calculate the result and then
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display it in the original window. For a simple calculation like plane fit, once the background has
been subtracted there is no point in performing a second plane fit because nothing will happen.
The second instance is where a subsequent process will produce different data (smoothing, etc.) ;
in this case, the dialog box will be different. When this occurs, it is important to understand the
difference between performing the process in a sequential manner or on the original data. The
dialog box for these processes will have three buttons. The first will Cancel the calculation and
also should be used to close the window when the calculation is complete. The second button
will Undo the previous result, the third will Calculate the result. There will also be two radio
buttons labeled Original and Sequential. When sequential is selected, each time the Calculate
button is pressed, the data in the window will have the process applied again. In this manner, a
single image could be smoothed numerous consecutive times resulting in the noise being
progressively reduced until the visual appearance is satisfactory. At any time during the process,
the Undo button can be pressed and the series of n steps reverses by one step so the displayed
image is the result of n-1 steps. If the data has been
changed so much that a single step undo is not
sufficient, then the Original radio button should be
pressed so the next calculation that takes place will
be the dataset when the process was first chosen
Figure 93
and the displayed image will be the result of only
one process. If the Original button remains
checked, then subsequent clicking of the calculate
button will not change the data because it is always the result of a single process. To return to
processing the data sequentially, click the sequential button and press Calculate to increase the
number of times the process has been applied to the data. Note that the Original button returns
to the data when the process was chosen which means if other steps had already been done by
other routines, the Original button does not go all the way back to the raw data, it only goes
back to the dataset when the menu item was chosen.
There is a method to return to the original
unprocessed data regardless of all steps that
had been performed up until that point. This
uses the icon shown on the far right side of
the toolbar in Figure 93. If data has been
changed due to any process, this icon will be
shown in color and it can be clicked to return
to the raw data. Even if processed data has
been saved in the SM3 file, the originally
acquired data is still saved in the file (part of
the new SM3 file format) so it is never lost.
This can be a tremendous advantage if months
after the data was taken it was realized the
images were processed using a faulty series
of steps. That data can be thrown away and
the unprocessed data used as a starting point
to redo the correct sequence of steps.
Figure 94
The simplest data processing step is the
Plane Subtract. A linear plane is fit to the
data using a least-squares algorithm and
then subtracted from the data. The equation
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used is ax+by+c. It only makes sense to perform this one time on any piece of data. A slightly
better routine for some data is found using the Parabola Subtract where a two dimensional
hyperboloid is fit to the data and then subtracted. This can help eliminate effects present when
scanning large distance using tube scanners due to the curved surface the scan plane follows.
The equation used is ax2+bxy+cy2+dx+ey+f. This step also only makes sense to be performed
once. To open the window shown in Figure 94, right click on an image and choose
Process/Background/Parabola Subtract. When the window first opens the coefficients are all
equal to zero. To have the software automatically subtract the best fit plane or best fit parabola,
click the appropriate button. At any time, the individual controls can be changed to have manual
control over the subtracted background. Of course, if the second order terms are all set yo zero,
then a plane will be defined and subtracted from the image. If other derived data is present on
the screen (sections, histograms, 3D renderings, etc.) as the background subtraction coefficients
are altered manually, the other data representations of the image will also update in real time.
Often it is easier to decide the best subtraction by looking at a section or the histogram,
particularly when the image has steps in it, by using this other data. When the line section shows
flat terraces and when the histogram shows distinct peaks the image will accurately represent the
real surface with terraces separated by the correct value based on the know crystallography.
Instead of manually adjusting the background of a terraced surface, the built in Step Flatten
routine can be used to get an image with flat terraces from an area of the surface containing
steps. This routine fits a parabola to the flat terraces only. When the dialog box (Figure 95) is
opened for this process, it is recommended to leave the Original button checked so the
calculation is performed on the raw data each time (as the settings are tweaked for optimal
results) instead of “flattening” an image that has already been flattened. After changing either or
both parameters click the Calculate button to perform the function and view the new result in
the original window. The Step Flatten Threshold determines how flat a “flat” terrace must be
in order to contribute to the calculation. Too small of a value here will result in an unstable
calculation, but too large will not achieve the desired result. For images with broad terraces and
few steps, try a value greater than one. Step Flatten Smooth determines the number of pixels to
use to determine if a region of the surface is smooth or lies at a step. The smaller the number, the
longer the calculation time. This algorithm was graciously provided by Dr. James C. Dunphy.
If X Offset Subtract is chosen, the mean value of each line is subtracted on a line-by-line basis
for all data along the x axis, and this can be used to reduce low frequency noise in the data. The
average value of the entire data page is kept constant though since there are cases where this
value has physical meaning. This is most commonly used to remove offset in an image due to an
instantaneous tip change where the z piezo adjusts up or down a significant amount because the
overall length of the tip has changed when scanning along the x axis. To remove the slope of
each line of data along the x axis, use X Slope Subtract. However, it is far superior to use the
hardware slope compensation to remove as much slope as possible along the fast scan direction
before the ADC when acquiring topographic data. Since this is not possible for any other data
channel, the image processing step is quite useful for those images.
If Y Offset Subtract is chosen, the mean value of each line is subtracted on a line-by-line basis
for all data along the y axis, and this can be used to reduce low frequency noise in the data. The
average value of the entire data page is kept constant though since there are cases where this
value has physical meaning. This is most commonly used to remove offset in an image due to an
instantaneous tip change where the z piezo adjusts up or down a significant amount because the
overall length of the tip has changed when scanning along the y axis. To remove the slope of
each line of data along the y axis, use Y Slope Subtract. However, it is far superior to use the
hardware slope compensation to remove as much slope as possible along the fast scan direction
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before the ADC when imaging the topography channel.
To remove features that are large in extent (creep, nonlinear scan plane from a piezo tube, etc.)
use the High Pass Subtract routine. All features longer than the distance entered in the
parameter window (Figure 96) are removed from the
image. This is another process where it is recommended
to set the sequence radio button to Original.
Use the Background Zero function to set the value of the
center, mean, median or mode of the image ADC range to
zero. The zero mode is set in the control window
discussed below. A selected region can also be defined
for the zero function. This function is useful for
Figure 96
comparing image heights in cross sections, setting a
particular terrace to zero, subtracting a background in
NSOM images, removing offsets in friction images, etc. It
should not be used on images where the absolute value of Z
is significant, for example STM current images.
Instead of performing the fit and subsequent subtraction to
Figure 97
the entire dataset, a small region of the data page can be
chosen for the fit. The coefficients are then used to calculate
the fit for the entire data region and the
subtraction is then performed. This can be
useful if noisy regions are present in the data
that severely effect the quality of the fit when
the whole image is used, and can also
improve the fit to the data if there are a large
number of terraces in the image and the Step
Flatten routine above does not give
satisfactory results. The first step in this
process is to define regions to include or
exclude from the fit. Click either the Include
Region or Exclude Region button ( at Far
right of Figure 97) and draw a box. As more
boxes are drawn, each region will be defined
by the button that is currently highlighted.
The box changes color to indicate if it is to be
included or excluded. If the area is to be
excluded, then a white box is outlined, while
an included region is surrounded by a green
box as shown in Figure 98. To start over
Figure 98
again with region selection, click the Erase
all Regions button to remove all boxes and
then outline new regions using the same method as above. When all region selection is finished,
click the arrow cursor icon to return the mouse cursor to normal mode. Then select
Processing/Define Back to perform the background subtraction with the fit only performed to the
included regions and then extended to the entire image area. The routines used are identical to
the ones described above that are used for the entire data page.
Use Smooth Image to eliminate noise spikes by simply replacing each pixel with a value
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calculated using a two dimensional weighted average of the nearest neighbor pixels. This
procedure will be performed on the preceding result each time the Calculate button is pressed.
Pressing multiple times will lead to progressively smoother and smoother images. If Fast Scan
Smooth is selected, the image is smoothed by performing the routine only along individual scan
lines in the fast scan direction. This can be preferable to the routine described above if the
experiment involves successive scan lines being considered pseudo-independent such as
diffusion experiments where the lines are a time dependent ‘snapshot’ of the local surface. This
avoids mixing pixels in the y direction where there should not be expected to be any
relationship. The number of pixels to average together is chosen in the dialog window that
opens. The routine can be performed sequentially or on the original data using the radio buttons.
To enhance some features like steps or abrupt transformations, the Sharpen Image routine
should be used. It will enhance edges by
adding an amount equal to the local slope
(calculated using a Laplacian routine) to each
pixel. Single pixel noise “spikes” in the data
are best eliminated using the Median Filter
selection.
Processing images in Fourier space
When periodic features are to be suppressed
(noise removal) or accentuated (atomic-scale
lattice reconstruction) it is advantageous to
calculate the FFT of the system and then
apply filters in Fourier space. This can be
accomplished using the Fourier tool in
XPMPro. Right-clicking on an image and
choosing Fourier View will open a four panel
window as shown in Figure 99. The original
image is displayed in the upper left panel, and
its 2D FFT is shown in the upper right. The
lower right panel is the 2D FFT with the
Figure 99
filtering applied and the lower left quadrant
displays the final result with all processing
applied. A control window is also opened as
shown in Figure 100.
There are three tabs included here. The Filter tab
can be used to apply a low pass, high pass, or
bandpass filter. A fourth option is to apply no filter
at all, which is chosen by setting the Filter Type
parameter to No Filter. As the cutoff dimension is
changed, the third pane will display the result. An
example of suppressing small features is shown in
Figure 101. The smaller features will be at larger Figure 100
spatial frequency values which in Fourier space are
farthest away from the origin (center of the image). All values above the cutoff have been set to
zero which is represented by the dark color in the outer region. The abrupt difference illustrated
here is due to the choice of Ideal for the Filter Cutoff parameter. This is similar to a step
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function whereby all values outside the cutoff are multiplied by 0 and everything inside is set to
1. Other filter shapes that can be chosen are 2nd order, 4th order, and 8th order. These roll off at a
specific decay shape so the values outside the cutoff are multiplied by decreasing values until the
factor does eventually become zero and provide a smoother transition in the resulting FFT so the
inverse FFT is less likely to have artifacts introduced due to the finite size of the two
dimensional array. Compare the shape of the four different cutoff shapes displayed in Figure
105. Note the second order filter has a very slow decay and the FFT shows only a slightly
darkened area near the middle. The 8th order has a more abrupt drop so there is a more
substantial region in the middle where all the power has been removed.
A nice example showing the effect of suppressing
large features is illustrated in Figure 102. Here
Suppress Large Features was chosen and a small
circular region near the origin is set to zero. This
removes the large terraces from the original image
leaving only the periodic noise due to vibrations in
the image as seen in the lower left image. There are
a variety of applications where this could be very
useful. Removing a long wavelength background
from the image, removing a long wavelength charge
density wave while leaving the true atomic
locations, etc. The opposite procedure also can be
useful, that is removing short wavelength features to
leave other structure visible such as removing
atomic scale variations to better highlight long
wavelength structure such as charge density waves,
Figure 101:
periodic steps, heterostructure topography due to
electronic effects, etc.
If there are obvious noise features in the image but
also important features with approximately the same
spacing, the filters may remove the noise but also
remove the important parts of the image. In this case
the tools available in the Point tab may prove more
useful. These can be thought of as an eraser to
remove isolated peaks in the Fourier plane which
will then remove the periodic noise in the final
image. The angle of isolated peaks with respect to
the x axis can be thought of as the phase of the noise
which is related to the angle of the features with
respect to the image axes.
The sample image used up until now can provide a
nice example of this powerful tool. The two bright
peaks in quadrants 2 and 4 are obviously the
periodic “rows” seen angling from the lower left of Figure 102:
the image to the upper right. This structure was
created by vibrations in the instrument producing a
modulation of the tip sample junction that the feedback loop was trying to null out.
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2nd order
8th order
Figure 104
Figure 103
Blotting out these two peaks will totally remove
the rows from the image and leave only the underlying gold terraces visible. The first step is to
change to the Point tab and choose a shape to draw on to the FFT. The Circle shape works very
well for most applications since the peaks are usually circular is shape in Fourier space. Once the
shape has been chosen, place the mouse cursor in the upper right panel and click and drag the
mouse to draw a light blue circle in the image. After it has been sized correctly using the small
handles, it can also be moved by clicking anywhere inside the box and dragging it to a new
position. Figure 106 Is an example of removing four peaks to clean up the image. The most
prominent noise is removed using the largest circle. Secondary noise peaks very close to the y
axis were subsequently removed to erase some higher frequency noise apparent after the initial
removal. The end result is shown in the lower right quadrant and is a much improved image.
For noise peaks with a varied shape in Fourier space, two other tools are available, the ellipse
and the rectangle. The ellipse is similar to the circle tool but it useful of the peak is elongated in
one of the two coordinates of Fourier space. The
rectangle can erase a wide range of power at
between specific x and y spacing values given
the 2D FFT is also graphed on an orthogonal
coordinate plane.
Three-dimensional rendering
XPMPro can display any image page as a threedimensional rendering combined with the
proper lookup table relating height to color.
This provides a nice view of relative feature size
Figure 105:
as well as shape. To produce a 3D rendering,
choose Plot/3-D view from the shortcut menu.
A window will open with the image rendered from a
point of view determined by the default parameters
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Figure 106:
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in the 3D Settings window () opened from any 3D plot. The 3D Tilt is the angle from the
horizontal plane. A value can be entered directly or the scrollbar controls may be used. The 3D
Rotate is the angle the x axis forms from the bottom edge of the window frame. Z Scale is a
factor that can be used to accentuate vertical heights in the image. Values greater than 1 will
make all features look taller than reality and values less than 1 will make all of them smaller than
reality. Line Skip is used to render the images faster on slower machines. Instead of forming the
image from every scan line, every nth line can be used which reduces the image processing
calculation needed to render more lines of data. Most modern computers can easily handle the
requirements such that the value can be left at 1. Mode determines the type of rendering to draw.
Fill will create a solid surface. X Line will draw the data with lines following the x axis. Y Line
will draw the data with lines following the y axis, and Mesh will render the data with lines in
both directions to form a grid of points on the image. Use the Apply to radio button to choose
whether all 3D plots on the screen should be changed to show the same viewpoint of if only the
currently selected one should use the new settings.
Instead of using the dialog box to determine the optimal settings, the values can be chosen
interactively by selecting the Interactive 3D menu choice from the shortcut. The window will
change appearance and as the mouse cursor is moved vertically, the tilt angle (Θ) changes. As
the mouse is moved horizontally the rotation angle (Φ) changes. The current readings are
displayed at the top of the window as illustrated in Figure 106. To increase the z scaling factor
hold down the left mouse button and release when the scaling looks good. To decrease the
scaling (make flatter) hold down the right mouse button. When the angle and scaling looks
correct, double click the mouse button to return to a normal 3D window view.
The Chart/Wire View selection will change the image so
each line scan is offset from the previous one to form an
image. This is reminiscent of the early days when STM data
was acquired using a chart recorder. An example is shown in
Figure 107. The Chart Settings dialog box can be opened by
right clicking on the image. The z scaling factor and whether
scan lines should be skipped when rendering the chart data
are configured in this dialog box.
The New Plot menu selection creates a new data window
with the same data representation as the original window. The
second set of data can be used to change the color lookup
Figure 107
table, the mapping of height to color, background subtraction
processes, etc. and the result compared to the original
appearance still present on the screen.
An interesting way to represent the data can be achieved by utilizing the 3D Dual choice. After
this is chosen, the cursor changes shape and the user should click on the first image which will
be used to form the shape of the 3D rendering. However, the color representation will come from
the second image chosen. This is a nice way to overlay one type of data with another to look for
correlations. For example, a topographic image could be used to form a shape and the friction
image used for color and the brightest colors should also appear exactly at the step edges when
the cantilever deflection is maximum.
Exporting data
Any image formed by an SM4 file can be exported in a common graphics format for importing
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into other programs. The valid graphics formats are bitmap, encapsulated postscript, PCX, TIFF,
JPG, and PNG. In addition there are also options for exporting the actual data in integer format
(RAW) and ASCII which is most commonly used for exporting XY graphs in column format.
To export data, use the toolbar button shown in Figure 108. The arrow can be clicked to open
the dropdown list used to choose the graphics format. The cursor now changes
appearance and clicking on a window will open a file dialog to provide the
filename and location of the exported image (or graph). XY plots, two
dimensional images, and three dimensional images can all be exported in
graphics mode. If ASCII is chosen, the most likely choice is to click on an XY
plot. Now the data used to form the plot will be written to a file in columns with Figure 108
the x axis in the first column and all displayed plots in additional columns. This
is done so the data can be imported into a separate graphing package for display or additional
processing/analysis. If a plot is selected and the export mode is NOT ASCII then the display of
the plot as composed in XPMPro will be written to a file. To exit export mode, click the button
which will make it appear unchecked again. The same function can be accessed using the
File/Export function and choosing a format. In this case, the Escape key can be pressed to exit
export mode.
If choosing a graphics format, a file save
dialog is presented as shown in Figure
109. The destination directory is selected
in the top section and a filename is
suggested based on the source file. This
can be changed if desired.
The bottom section of the window allows
the size of the graphics file to be
controlled. The number of pixels in the
graphics file can be determined via three
methods. It can be set to an arbitrary size
selected by the user using the Image
Dimension setting. An advantage of this
method is every file exported will have
the exact same size to easily combine
them into a movie regardless of the image
acquisition conditions or the size of the
window on the screen. The second choice Figure 109
is Pixel Dimension and this will create a
graphics file with a one-to-one correlation between an image acquisition pixel and graphics
output pixel. As the example shows, a 512x512 image is going to be exported so the entry box is
already filled in with that value in case the user decides to select it. The final selection is
Window Size which creates a graphics file precisely the same pixel size as the image window
currently occupies on the screen. This may be useful to prepare images for presentations and
desire to know the physical space on the screen they will occupy when imported into other
programs for page composition.
The overlay checkbox should be selected if various annotations that have been added to the
image should be present on the output file. Examples of this are the lines in an image that
represent extracted data sections, the array of dots added during lattice correction cursor mode,
the scale bar, and spectroscopy locations drawn in spectroscopy mode cursor view. To have
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purely the image pixels only, leave this box unchecked.
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Advanced Techniques
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In this chapter a discussion of various data acquisition methods are presented. Many of these
procedures are covered very explicitly in publications and books on SPM. Only an overview that
describes how to take the data with RHK equipment is presented here. For in-depth details of
certain experiments, other references should be explored.
One of the fundamental techniques used to investigate surface electronic structure is to acquire IV spectroscopy. This is accomplished by
interrupting the feedback loop and ramping
the applied bias while recording the tunneling
current. The resulting behavior of the junction
can provide insight into the surface density of
states as well as other interesting phenomena
related to the tunneling process itself.
There are some important precautionary steps
that must be taken to insure that the data does
not contain any artifacts introduced by the
acquisition routine itself. Because of
unavoidable capacitive coupling between the
bias and the tunneling current, whenever the
bias is changed, the rate of change dV/dt will
induce a transient current in the system. The
typical behavior is depicted in Figure 110.
This graph is a display of the bias voltage as a
function of time. The small voltage steps used
to move between voltage increments are not
Figure 110
shown for clarity, but the voltage does not
jump from one value to the next when using
XPMPro. Instead, the voltage is stepped at the 16 bit resolution of the board in order to decrease
the effective dV/dt rate that would occur if the voltage changed in one step from one plateau to
the next. The large constant value at the far left is the voltage while the feedback loop is on and
the topographic data is acquired. The feedback loop is then opened and the bias changed to the
first value of the ramp. This can sometimes be a large ∆V in a short ∆t so the transient has a
large magnitude. Decreasing the setup rate can reduce the magnitude of the transient because
the voltage will be changed to the initial value at a slower rate instead of one immediate jump. It
is a good idea to make the first voltage step as close as possible to the feedback bias so the initial
transient signal is minimized. After this decays away, the current reaches its equilibrium value
that is solely a function of the magnitude of the bias. After the current is sampled for a fixed
amount of time, the bias is changed to the next point on the ramp. The current is read
samples/point times after the initial pre-sample delay (t2 ) has passed. The small ∆V at each
voltage step induces a smaller, but still significant, transient signal on the current. Making the
sweep rate slower will decrease the amplitude of the transient present at each voltage step, but
every point along the voltage ramp will have this small, unavoidable transient signal. After the
current has been read at the last voltage step, another (usually) large ∆V is applied to return the
bias to the feedback condition which in turn induces a large transient. The loop is then turned on
again and the tip moved to the next pixel location.
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Because of these undesirable transient signals present in the current sensing circuit, a series of
fixed delay times are entered into
the control window used to setup
the I-V parameters. This window is
reproduced in Figure 111. It is very
important to carefully study the
response of the current signal to the
voltage changes in order to make
sure the delay times are long
enough to let all transients decay to
zero before sampling the data. If the
transients do not completely decay
away, not only will the data have an
extra offset at each voltage step, but
potentially the offset could change
at each step as the transients slowly
add up more and more as the ramp
progresses. This situation is
illustrated in Figure 112. The dotted
line indicates the nominal current
Figure 111
that should be present for a given
tip-sample bias but the solid line
represents the actual data. Notice how the signal level deviates by a progressively larger amount
at each voltage step since the equilibrium condition is not met at each ramp value, and the next
transient is added to whatever value the signal has decayed to instead of the baseline,
equilibrium value.
The acquired curve should be checked to see
whether the tunneling current when the voltage
value is near the tunneling bias is close to the
feedback setpoint. If this is not the case, the two
most likely causes are either there is significant
drift in the z direction during the time the
feedback loop is off or the delay times are not
long enough and an artifact related to the
addition of the transient signals as shown in
Figure 112 is present. If the voltage step is not
sufficiently long to allow the transient to decay
at each step, the recorded data will have this
accumulated error at each sweep value.
The three time parameters shown in Figure 110
should be adjusted in the window. The first
delay, t1, is determined by the Spectrum delay
setting. The delay at each individual voltage
step (t2) is set using the Pre-sample delay, and
the amount of time to spend averaging the
current reading at each step (t3) is determined
by Samples/point and Sampling time.
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A particularly useful feature is the ability to examine the individual I-V curves acquired at each
pixel. Occasionally, a large current spike may appear in a single curve because of some
anomalous event. This curve should therefore be eliminated from the rest of the acquired curves
that are selected to average. Many times, the reading at a single voltage step along a single curve
is so large that averaging the rest of the curves together still does not completely eliminate the
effect, but simply throwing that curve out and using the rest of the data to average away random
noise can dramatically improve the signal/noise ratio and the quality of the data.
Increasing resolution
The SPM 1000 system uses a 16 bit A/D board to read the data, and this limits the dynamic
range of any measurement. However, the resolution of any single measurement can be increased
if the data will vary over only a small range.
The overall gain of the tunneling current system is determined by the first and second stage
preamplifiers used to convert the tunneling current to a voltage. The largest voltage range that
can be input to the electronics is ±10 V. The preamplifier gain and this voltage together
determine the maximum current
that can be detected. For an
overall gain of 108, the
maximum current is 100 nA and
if the gain of the ADC board is
not increased, the least significant
bit (LSB) when acquiring I-V
data would be 3.05 pA. The
resolution of a measurement can
be increased by changing the gain
of the ADC board for the channel
to be measured.
The window controlling the gains
is shown in Figure 113. The
maximum voltage range to read
for any channel can be changed
by setting the appropriate range
parameter as shown in the
window. Valid choices for any
Figure 113
channel are ±10 V, ±5 V, ±2.5 V,
±1.25 V. If the signal will be
changing over a reduced range, then it is advantageous to increase the gain in the measurement
by changing this setting during the I-V acquisition. If the range is changed to the smallest setting
of ±1.25 V and an overall gain of 108 is in use, the LSB will be changed from 3 pA to 0.38 pA
because the 16 bit resolution will now range over readings from -12.5 nA to +12.5 nA.
As long as the maximum current will not exceed these values and saturate the ADC, then the
increased resolution makes it well worth changing the parameter. Even if a large tunneling
current is used, high resolution spectroscopic data can be acquired by using a voltage sweep
where the maximum value is below the bias voltage used when imaging. Very high resolution Iz data can also be acquired using this functionality and this can be very important given the
exponential dependence of the current on the distance the tip is moved. The tip can be retracted
from the sample and the decay of the current accurately recorded since it is known a priori that
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the tunneling current will only decrease as the tip is pulled away from the surface. On the other
side, we also can increase the bias slope resolution by attenuating the bias at a place near the
scan head. For example, our interesting area of the bias is only in a range of -0.1 V to 0.1V, we
can attenuate the bias to 1% at a place near the scan head. Then input sample bias per monitor
volt at Figure 4 and output units per D/A volt at Figure 51 are set to 0.01 V. These will increase
the output accuracy.
Variable gap spectroscopy
One of the main problems associated with acquiring I-V spectroscopy, particularly when
studying semiconductors, is sensitivity to very small currents. In the case of semiconductors, the
current will approach zero as the bias nears either edge of the bandgap; while for other materials,
the current will be small near zero bias. This sensitivity limit can hinder the detection of features
near the band edges (or in the bandgap) and even the precise location of the band edges
themselves. For example, if the maximum detectable current is 100 nA (a typical figure for most
microscopes), for a 16 bit ADC, the least significant bit (LSB) will be equal to a value of 3.05
pA. One way to increase the lowest detectable current is to increase the gain in the first stage
amplifier, which can be accomplished using the IVP-300 preamplifier from RHK. This leads to
an increased gain in the circuit but the maximum detectable current would then be equal to only
10 nA. When this is spread over a 16 bit ADC, the LSB is then 0.305 pA, but no increase in
dynamic range is realized since the maximum current has been decreased by a factor of 10 in
order to gain a factor of 10 increase in the smallest detectable current.
This limitation can, however, be surmounted by taking advantage of the exponential dependence
of the current on the width of the tunneling gap. For a typical vacuum barrier under clean
conditions, the current will increase by about an order of magnitude for every 1 Å decrease in
the tip-sample separation. This means that if the feedback loop is opened and the tip moved
towards the sample as the bias is lowered, the minimum detectable current will effectively be
increased. The maximum current would still be 10 nA at any particular time, however, since the
current gets very small as the
bias is decreased, the tip can be
moved towards the surface. This
will lead to an increase in the
measured current. After the data
has been acquired, it can then be
renormalized to represent a set
acquired at a single gap width by
dividing the measured readings
by a number related to the
amount the tip was moved
towards the sample at each
voltage step. Since this number
will be larger than 1, the current
readings at the low voltages will
decrease in value. Because of the
exponential relationship, moving
the tip 2 Å towards the surface
will mean the current readings
acquired at that separation need
Figure 114
to be divided by a factor ~100 to
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be compared to the values acquired at the nominal tip-sample separation under feedback
conditions. If the current readings are around 0.5 pA (still above 1 LSB), the normalized current
will actually be equal to 0.005 pA or 5 fA. When the entire data set is combined into one curve
the data can easily range from the maximum near 10 nA down to a few femtoamps or lower.
This represents a total dynamic range of 6 or 7 orders of magnitude, which would normally
require an ADC with about 22 bits.
The voltage applied to the z piezo as the bias voltage is ramped is shown in Figure 114. The
lower graph is the bias ramp and the upper curve is the voltage added to the z piezo with the
convention that a positive voltage pushes the tip towards the sample. The magnitude of the
voltage applied to the Z piezo is determined by the Z change per bias volt. This, in effect,
determines the overall slope of the upper graph. A large number will push the tip towards the
surface very quickly as the voltage is lowered, whereas a small number changes the gap very
little as the voltage approaches zero. There is a delicate balance that requires some
experimentation to determine the best settings for any particular situation. If the number is too
large, the current will increase too rapidly as the tip approaches the sample and there is a danger
of damaging the tip and/or sample by creating too large of a current density. Potentially, the
current could also be above the ADC maximum which will lead to useless data since the
readings will saturate. If the number is too small, the current will continue to decrease towards
the LSB and an insufficient gain in sensitivity may be achieved. A good rule of thumb would be
to start with a slope such that the difference between the feedback bias and the voltage where the
current will be near zero (the band edge for a semiconductor, zero for other conductors)
produces about 2-3 Å of motion towards the surface. For example, if the tunneling bias on a
Silicon surface is -1.5 V, to produce a 3 angstrom decrease in the gap width would require the Z
change per bias volt be set to 2.
The proper series of steps to perform when setting up spectroscopy data acquisition would be to
acquire some I-z spectroscopy curves to measure the attenuation length of the current tip-sample
combination. Then obtain some I-V data with a fixed tip-sample distance over the entire voltage
range, and finally, acquire the variable gap data and compare it to the first set of I-V curves to
check for close agreement between the current readings at large values of the applied bias (the
beginning and end of the voltage sweep).
Stabilize Drift
When parking the tip over a feature and acquiring spectroscopic data to investigate the electrical
characteristics, there is a never-ending struggle between getting high quality data and staying
over the feature of interest. The more readings acquired and the slower the voltage is ramped, the
better the data. However, this also takes more time. Since all microscopes exhibit some relative
motion between the tip and sample over time, the longer the acquisition takes, the confidence in
staying over the feature for the duration of the experiment decreases. This delicate balancing act
has a new weapon to combat the effect. In version 2.0 of XPMPro, it is now possible to stop the
spectroscopy sweeps, rescan a small area of the surface, locate the feature of interest, and apply
a correction voltage to insure the tip remains over the feature sweep after sweep after sweep.
Note this only makes sense if the spectroscopy is one of the point modes and not within an
image scan. To activate the algorithm, choose XYZ Stabilize in the Advanced Modes tab for the
active spectral mode as shown in Figure 115.
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After configuring the spectral mode, the next step is to acquire an image and load it into the
NAV window to know where the
feature is located. Next the Spec
Location pane should be opened
and the Spec Location parameter
changed to Drift Ref. A cyan box
with a small green box inside will
appear on the screen. Use the
mouse to select each box and
resize them appropriately. The
green box should be placed
around the feature of interest and
the cyan box should be large
enough to make sure the feature
does not drift outside this region
between rescans. The larger the
search area the higher the
likelihood of finding the feature,
but the longer the scan will take.
XPMPro will determine the
number of pixels included in the
Figure 115
cyan box given the currently
loaded image's pixel density. As
the boxes are resized and moved, the Scan Area,
X Offset, and Y Offset entry boxes display the
values for the spectroscopy box instead of the
normal imaging box. Once the Spec Location is
changed to any value other than Drift Ref, the
entry boxes return to displaying the normal scan
area parameters. It can then calculate the required
time to obtain an image this size at the presently
configured scan speed. An example of a selected
feature and a scan area box is shown in Figure
116.
After defining the feature and the search area,
place the tip in the location containing the feature
to be studied. Note, the tip does not have to be
located within the search area. The feature to be
studied may be offset from the search feature and
after locating it each time, the tip is moved to the
same relative position with respect to the located
feature so it is placed over the correct feature. In
effect, as long as the two items (drift reference
feature and spectroscopy feature) do not move
with respect to each other, as one drifts the other
drifts the same amount. However, if the
spectroscopy feature has a unique appearance it
Figure 116.
is recommended to use it for the drift feature also
for simplicity and a reduction in tip movement.
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When the spectroscopy start button is pressed, the first action is to acquire the small image
defined by the cyan box. Then the stored feature inside the green box is fit to each location
inside the just acquired image and the best fit is interpreted to be the feature location. If this is
offset from its original location the search frame is shifted. The tip is then moved to the new
feature position, the loop is opened, and spectroscopy data acquisition starts. Either one curve is
acquired or a group of curves are acquired and then the loop is closed and the tip scans the
surface to acquire another image. The pattern matching algorithm again matches the original
feature location to the present feature location and any necessary shift is applied. This sequence
of steps continues until stopped.
Whether to correct for lateral drift between each curve or after set of curves are acquired, is
determined by the Each Spectra/Each Location radio button. If Present Position is the selected
mode, a set of curves is specified by the Curves to Acquire parameter in the spectroscopy setup
window. If the drift rate is small and there are not too many curves specified, it is safe to only
correct between a group of curves. If the Save button is pressed during the acquisition or
Autosave is active and the group of curves are to be saved in an SM4 file, the small image
acquired before the curves is also stored with the file so at a later time a high degree of
confidence can be assured that the data was taken with tip over the feature.
While the acquisition is taking place the last tab of the spectroscopy graph window can be used
to view the original image and the feature determined to be the best fit side by side (Figure 117).
This can help decide if the acquisition should be stopped. If the most recently acquired image no
longer appears to match the original image very well, the tip is most likely not directly over the
feature of interest and there is little point in
continuing with the acquisition. The total
accumulated drift during the duration of the
spectroscopy is also displayed below the pair
of images.
Conductance measurements
By applying a small modulation on the
tunneling bias the change in current as a
function of change in voltage can be
acquired. The simplest way to do this is to
use a lockin amplifier and apply the
Figure 117.
excitation signal to one of the rear panel bias
modulation inputs. Then the output of the rear panel preamp monitor BNC is connected to input
of the lockin and the output of the lockin that is proportional to the amplitude of the current
modulation is attached to one of the rear panel auxiliary channels.
Conductance maps of the surface can be acquired by measuring the output of the lockin at each
pixel. The scan speed has to be slowed down enough to give the lockin amplifier adequate time
to reach its new equilibrium at each pixel. The amount of time to spend at each pixel in the
image should therefore be 2-3 times the value of the Time Constant setting of the lockin
amplifier.
Conductance curves as a function of voltage can be acquired by reading the output of the lockin
at each point along the voltage sweep as the current is also recorded. For this, the current and
auxiliary channel should be checked in the input tab of the spectroscopy setup window. Also, a
presample delay will have to be set for this experiment in order to allow the lockin to reach its
equilibrium value. This delay should be about 2-3 times the Time Constant set for the lockin.
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Taking images can be tricky because the amplitude of the lockin output depends somewhat on
the oscillation frequency. The chosen frequency has to be
above the bandwidth of the feedback loop so the
modulation of the tunneling current due to the modulation
of the bias is not corrected by the feedback loop. Typical
values would be a frequency from 5 kHz to as large as 20
kHz or so. The Time Constant of the lockin should be long
enough to span at least a few complete oscillations of the
signal. For example, a 5 kHz frequency has a period of 0.2
ms so the Time Constant of the lockin should be at least
0.5 ms or more. For imaging this means the scan speed
should be slow enough that at least 1 ms is spent at each
pixel. For a 256 pixel image, this would mean a scan
speed lower then 200 ms/line is required. If acquiring a dI/
dV curve then the pre-sample delay should be at least 1 ms
before readings of the lockin output commence.
Figure 118: operation mode define tab
RHK PLLPro is an excellent candidate to perform the bias
modification and pick up the modified the signal. It
integrated function generator and lock-in amplifier to one
unit, and the controlling software is integrated in XPMPro
2.0. This electronic controller will introduced in detail in the
section of AFM. In the experiment, we connect the D/A
output channel 2 , channel 3 and channel 4 of PLLPro to
AUX input channel, channel 2, and channel 3 of stm100
respectively. The Probe drive out of PLLPro should be
connected to the bias modulation in stm100. We can use
XPMPro inset package to control the PLLPro. Here we only
introduce the related part we need here. Detail instruction of
the PLLPro can be found in the PLLPro manual and the AFM
manual.
First,we click the setting->operating mode, XPMPro 2.0 will
pop out a window as Figure 118 shown. We PLLPro Master
at SPM acquisition mode, and close it. Then we click on
view->PLLPro status, XPMPro pops out a window as shown Figure 119: PLLPro Control
in Figure 119. In the lockin mode, we set the driving
frequencies and the amplitude to modulate the bias. Set the amplitude setpoint as the offset of
lockin amplitude and amplitude with proper scaling to make the output fit to be digitized by the
stm100. We set the amplitude output through DAC2, and we also can set the phase setpoint,
amplitude and scaling as in the same way; then, we set the output through DAC3. Aux 1 and
AUX 2 input will be automatically named as amplitude and phase in XPMPro 2.0.
Then we can take Conductance measurements data through image scanning or spectroscopy.
Barrier height measurements using I-z spectroscopy
The quantum mechanical nature of the tunneling phenomenon results in an exponential
relationship between the tunneling current and the gap width. This is usually expressed as
I∝ e
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where k is a constant that depends on some physical constants as well as the mean barrier height
of the gap and z is the tunneling gap distance. The value of k, and hence the barrier height itself
can be determined by obtaining spectroscopy data. In this routine, the feedback loop is opened
and the tip is moved away from the surface while recording the current at each step. This data
will exhibit an exponential decay equal to 2k.
This data usually does not have the transient signals present compared to the I-V data because
there is little reason for coupling between the current and the z piezo position given a good scan
head design where the two signals are isolated from each other. It is usually a good idea to still
use a small pre-sample delay in the spectroscopy window to allow the piezo tube to settle for a
small amount of time after the tip has moved, but large peaks as seen in the I-V section above
are rarely seen.
The slope of an I-z curve when plotted on a linear (z)-logarithmic (I) scale can be determined by
a simple fitting routine and this would be used to calculate the barrier height. Once the slope, m,
is known; the barrier height is calculated using this equation
 =
m 2

1.025
Various features on the surface such as contamination or defects can create a local variation in
the barrier height and this can be seen by acquiring I-z curves in two distinct regions and
comparing the value of Φ derived from the two sets of data.
Additionally, as described above this data is also used to determine the attenuation length that is
needed for proper normalization of variable gap I-V spectroscopy data. The correct value can be
ascertained by simply looking at a plot of the I-z data and noting the ratio of two current
readings that are separated by a given distance. Select any current value and then find the value
that is e-2 times smaller.
Barrier height measurements using a lockin amplifier
As discussed in the previous section, features on the surface can change the local work function,
and this can be measured with a STM. A direct correlation between the topographic structure
and the work function can then be obtained. The best method to acquire this type of data is to
apply a small oscillation to the z piezo so the tip-sample distance oscillates a small amount. If
the modulation frequency is high enough that the feedback loop cannot compensate for it, then
there will be an oscillatory signal superimposed on the tunneling current at the same frequency.
This can be monitored by a lock-in amplifier and the signal from the lock-in would then be
proportional to the local work function. If an image is formed of this signal along with a
topographic image, common features in both images can be correlated.
Some additional cables are required to connect the lock-in amplifier properly. The oscillation
signal out of the lock-in amplifier should be connected to Z modulation input #2, and the current
monitor output on the rear panel of the SPM 100 should be connected to the input of the lock-in.
The amplitude output of the lock-in should then be connected to one of the rear panel auxiliary
inputs. To simultaneously acquire the topographic image along with the output of the lock-in, the
auxiliary channel connected to the lock-in output should be turned ON in the Input tab contained
in the Settings/Scan window. For a more meaningful display of the barrier height image, the
label of the auxiliary channel being used could be renamed to something more descriptive like
“barrier height” or “amplitude”. This is done in the Settings/Operating modes/Define tab.
While the tip is scanned, the two input channels will each be sampled for an equal amount of
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time before the tip is moved to the next pixel. Both the topography and lock-in signal should also
be saved in the data files. The signal stored from the lock-in output then has to be converted
from Vout of the lock-in into eV of mean barrier height. The derivation of this scaling factor is
presented below.
From basic tunneling theory, we know the current is an exponential function with the form
I∝ e
−2k z
where
k is constant that includes the barrier height and z is the tunneling gap distance. A typical value
gives a decay of about an order of magnitude in current for every 1 Angstrom change in the gap
distance.
If we modulate the gap distance by a small amount δz using a sinusoidal function, then the gap
width will have the form
z=z 0 z cos  t 
and the tunneling current then has this form
I ∝e−2 z
0
 z cos  t 
which can be rewritten as
I ∝e−2 z ∗e−2  z cos  t 
0
If the modulation frequency is well above the bandwidth of the feedback loop, the first part of
the expression is simply the normal feedback tunneling current, I0. If the modulation amplitude
is small, then the exponential can be expanded via Taylor’s series to be
I ∝I 0 1 −2  z cos t 
A lock-in amplifier operates by taking the input signal and detecting the portion of it that is at
the same frequency as the output frequency (which in this case is being used to modulate the
height). Most lock-in amplifiers will output a signal that is equal to the rms value of the cos
term. For this situation, the amplitude of the signal is
−I 0∗2   z
This rms introduces an additional square root of 2 into the expression so the output signal will be
related to the modulated current detected by the lock-in amplifier by
−I 0∗2   z
1
2
Solving for k gives the expression
=
−I lockin
 I 0∗ z 1 /  2 
From a quantum mechanical derivation of tunneling, k will involve some constants related to the
electron and the mean barrier height Φ which becomes
2 =1.025 
substituting this expression into the derivation of k above yields
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
I lockin  2
=
 I 0  z 1.025

2
When the modulation is set on most lock-in amplifiers, the voltage selected is actually the rms
voltage applied to the z modulation, and this means the δz amplitude can be expressed as the rms
value of the modulation which is
 z=
z lockin
2
If we substitute this into the above expression, the (rather confusing) square roots cancel and the
final expression is

I lockin
=
 I 0 z rms 1.025
2

Measurement parameters
For some starting numbers, set the modulation voltage on the lock-in to 100 mV which should
correspond to shaking the tip a tenth of an angstrom. As the signal is increased, some ripple on
the tunneling current should appear when displayed on an oscilloscope. A frequency of a few
kHz is a good starting point. When the oscillation amplitude is increased, the output signal of the
lock-in amplifier should also increase since the amplitude of the current modulation also
increases.
It is a good idea to make a quick calculation while not scanning to see if the value for the barrier
height makes sense given the tunneling conditions. The conversion from the output voltage of
the lock-in amplifier into tunneling current should be whatever gain is in the system. If an IVP
200 is used which provides 108 gain and the IVP-PGA is set to x10, the overall gain is 109 V/A
so 1 V output from the lock-in corresponds to 1 nA current. If the output signal from the lock-in
amplifier is 10 mV (for example), then the resulting modulation on the current due to the z dither
is 10 pA (0.01 V / 1 V/nA is 0.01 nA which is 10 pA).
To calculate the local change over certain features, average the voltage output from the lock-in at
pixels that are over the feature to obtain one value. Then convert this to equivalent current as
described previously and this can then be converted to the mean barrier height using the final
equation above. This should be compared to the value obtained by averaging a large area over
the normal surface far from any defects.
Input/Output line-by-line imaging
A particularly useful feature of XPMPro is the in/out image spectroscopy mode. Imaging
conditions can be changed on an image-by-image or line-by-line basis. There are a plethora of
experiments that can be performed using this capability.
The main use for this is to measure friction forces using an AFM. The normal force can be
changed every line and the slow scan axis is disabled so the same area of the surface is scanned
repeatedly. If lateral force data is acquired, then the acquired image will be a record of the lateral
force as the normal force increases.
However, there are many other potentially useful experiments that can be done. One example is
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to use the output voltage to interface with a temperature controller. As the output voltage is
increased/decreased the sample temperature can change accordingly and an image then acquired
that records the change in surface character as a function of temperature. With the ability to
introduce an arbitrary time delay after the voltage change the sample can have time to reach a
new equilibrium temperature before data is acquired.
Another example is to use this in STM to quickly explore a large sample space of imaging
conditions. Figure 120 is an image where the DAC voltage is summed into the bias and the
measurement was setup to change the bias every 16 lines. With the 512x512 pixel image, this
means the voltage was changed in 32 steps from 0V to -2.0 V. The initial bias (controlled via the
front panel knob) was -1.27 V so the top part of the image was taken at -1.27 V and the bottom
section was acquired at -3.27 V. Notice the change in the appearance of the faulted and unfaulted
sections of an individual 7x7 unit cell. At the lower bias voltages (nearer the Fermi level) the
contrast is more dramatic and as the bias voltage increases, the contrast all but disappears. This
can be a great time saver as a single image can be used to quickly search for bias dependent
features on the
surface that
otherwise might take Vgap= -1.27 V
a much longer time if
changing the bias
using only the front
panel knob. Once an
image like Figure
120 is acquired, then
the bias knob can be
adjusted to the
desired value to
acquire entire images
that highlight the
desired voltage
dependence. Another
good example of this
would be to search
for adsorbates and
defects present on
the surface that only
Vgap=-3.27 V
appear at certain
voltages these could
Figure 120
be missed if they
change their appearance over a narrow range of voltages.
Force setpoint when using a commercial AFM
The versatility of the SPM 100 allows for the control of commercial AFMs such as the
Nanoscope® , Multimode®, or Dimension 3000 from Digital Instruments or the PicoSPM®
available from Molecular Imaging. These scan heads all require an extra unit to interface the
coarse approach mechanism to XPMPro.
A common source of confusion is how to use the “current” and “bias” settings on the SPM 100
along with XPMPro to determine the appropriate setpoint for feedback conditions. As discussed
in the AIM-MI manual, the feedback signal out of either of these AFM heads is a voltage
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proportional to the deviation of the laser spot from the center of the photodiode detector. The
“bias” signal is used as a control signal inside the head by comparing the output of the photo
diode to this input signal. The feedback signal out of the head is then the difference between the
position of the laser spot on the PSD and the “bias” voltage which would be equal to a different
location of the spot. Therefore, the “bias” can be adjusted to move the deflection of the laser to
any location on the PSD. As the laser spot is moved, the amount the cantilever is deflected is
changed, and since the cantilever acts as a spring, a larger deflection also means a larger force
exerted on the surface. The “bias” should then be considered as how hard is the probe pushing
on the surface similar to what the setpoint would represent.
When first learning to use the SPM1000 system with an AFM, the Bias knob should be set to
zero as well as the setpoint. This is the simplest mode and is analogous to typical operating
conditions suggested by commercial suppliers of AFM heads who recommend starting with an
out of contact output signal of ~-1.5 V to -2 V and using 0 as the setpoint. After acquiring an
initial F-z curve the actual setpoint force can then be adjusted.
Adhesion and other forces can be studied when using an AFM by obtaining force-distance
curves. These are obtained by interrupting the feedback loop and moving the z piezo a known
distance to alternately contact the surface and break the tip-sample contact while recording the
output of the photodiode. This Vout can then be converted into a force given the spring constant
of the cantilever.
To acquire the data, a spectroscopy measurement must be setup. Use the menu item
Settings/Spectroscopy to open the tab used to setup an F-z curve. A BNC cable should be
connected from one of the DAC Output channels to the Z Position Modulation Input #1. It is
most important to see the flat region at large z which indicates that the tip has pulled off the
surface. XPMPro considers a negative value to be decreasing the tip-sample separation and a
positive value to pull the two apart. When taking an F-z curve, if it is desired to push the tip in
first while remaining in contact, use a negative value for tip initial height. If it is desirable to pull
the tip off the surface
before data acquisition
commences then use a
positive value for tip
initial height. If the far
distance region is still not
flat, continue to increase
the positive limit value
until it is sufficiently flat.
After taking a few curves,
the initial and final values
can be adjusted so the
dynamic range of the
curve allows the relevant
features of the
coupling/decoupling to be
seen. Be careful not to
push the tip into the
surface by too large of a
value (a limit that has a
large negative value) or
Figure 121
the cantilever and surface
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can be damaged by applying too much force. Input a large enough value for the final height
though so a large linear region is visible. This is the most critical part of the curve that is needed.
An idealized F-Z curve is shown in Figure 121 and can be understood as follows. After the
feedback loop is opened, the tip is pulled back a large amount so it starts at large positive z (A)
with no tip-sample contact. As z is decreased, the tip suddenly is pulled towards the surface and
makes contact (B) via various attraction mechanisms so the deflection of the cantilever is down
from its equilibrium position. As z continues to decrease, the cantilever starts to deflect upwards
(C) and the relationship between z motion and detector voltage is recorded. This slope is the
critical information needed to convert the photo diode voltage into a z height. As z then reaches
its minimum value and starts to increase, the deflection starts to decrease (D) but the tip
maintains contact with the surface for a larger z because of capillary forces between tip and
sample. The tip eventually breaks contact (E) and snaps back to its equilibrium position. As the z
increases to a large value, the tip and sample are again separated by such a large amount that the
cantilever remains at its equilibrium position (F). Note the slope of the large separation part of
the curve is shown flat in this idealized picture, however in reality, there may be either an
upwards or downwards trend to it as z decreases due to longer range forces acting between tip
and sample along with oscillations due to laser interference with light scattered from the sample.
First, go to Settings/Operating Modes/AFM and input the spring constant of the lever; then set
the deflection sensitivity to 0 V/m. The slope of the linear section of the curve ( C or D) can then
be used to determine the force setpoint. The slope will be
Deflection
z
and since the force constant of the cantilever is known in terms of N/m the amount of force
exerted on the surface as a function of z after contact can also be calculated. The selected voltage
will then serve as the setpoint for pushing on the surface so the “Bias” should be set to the value
(in V) on the y-axis where the user wishes to operate the AFM.
For example, if the D region in Figure 121 ranges from +500 C to -150 C and from 50 mV to 700
mV. This gives a slope of 1 mV/C (displayed as 10 MV/m in the software) for the detector
sensitivity, and if the cantilever spring constant is 0.1 N/m, then the probe will exert a force of
10nN for every 1 Volt change in the setpoint. Keep in mind these numbers are for illustration
purposes only and may not closely represent any particular microscope design or specific
cantilever. If the calculated value for the slope is now entered into the deflection sensitivity
setting in the window described above, any F-z curves acquired after this will display the values
as nN vs. nm.
Changing the setpoint force using the setpoint knob
Once an F-z curve is acquired and
calibrated, the actual setpoint can be
changed and the different feedback
conditions will be apparent in a
subsequent F-z curve. Figure 122
illustrates an idealized F-z curve and the
flat region is at the level set before the
approach (~-2 V normally). Note the
curve goes through the (0,0) point as
expected. The horizontal axis is the
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relative z displacement from the piezo position when the feedback loop was opened. This should
be zero nm if the feedback is properly maintaining the setpoint which is zero Volts to begin with
as discussed above. Since the SPM100 setpoint knob is restricted to a voltage between +1.0 V
and -1.0 V, the range of possible setpoint forces is denoted by the hatched region.
If a different setpoint force is desired
while in feedback, the setpoint knob
can be turned. The top part of Figure
123 shows the setpoint moving down
towards the attractive regime. Since the
knob will be turned while in feedback,
the z piezo will adjust to maintain the
changing feedback level. The F-z curve
itself is like an isogram showing the
value of z for a given setpoint and the
X on the plot is meant to illustrate the
intersection of the desired setpoint with
the known F-z characteristics which
then determines the new z value. After
the knob reaches the new value, the
new z position (relative to the former
position) is indicated in the figure by
the vertical dashed line.
The subsequent F-z curve is shown in
the bottom part of Figure 123. Since all
Figure 123
F-z curves are taken relative to the z
position when the feedback loop was
opened, the setpoint value will intersect the z=0 axis as always. The X was reproduced on the
second plot to illustrate the intersection of the new setpoint value with the F-z curve and to
easily visualize the effect of changing the setpoint. The F-z curve itself is merely shifted left and
right as the setpoint knob is changed because the feedback loop will move the z piezo in order to
maintain the new desired feedback value.
Changing the setpoint force using the bias knob
Due to the restricted range of possible voltages that can be used for the setpoint, the Bias knob is
necessary to select force set-points outside the original region. If the initial out of contact voltage
is set to -2.0 V as usual, a force setpoint in the attractive regime, cannot be reached solely by
using the setpoint knob.
Turning the bias knob to change the setpoint will have a slightly different effect. Since the actual
signal from the AFM head is effected by both the position of the laser spot on the PSD and the
bias voltage (see AIM MI manual), as the bias is increased (made more positive) the laser spot
will move across the PSD such that the voltage result from the calculation circuitry decreases
(spot moves down). As the bias is decreased (made more negative) the voltage from the PSD
will increase (spot moves up).
The effect of this would be to shift the F-z curve up and down relative to its original position as
much as +10 V or -10 V when the bias range knob is placed in the 10V position. However, since
the feedback loop is active as the bias knob is changed, the F-z curve will not shift directly up or
down because the setpoint and current z position would no longer intersect at (0,0) as marked by
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the X. As the F-z curve shifts up or down, it will also shift laterally such that the F-z curve
always goes through the origin of the plot (since setpoint=0 and z=0 always corresponds to the
setpoint force). A subsequent F-z curve after the adjustment will appear as the bottom part of
Figure 124 where the X was left on the graph to indicate the original force setpoint. The entire
curve has moved up and over as the bias is moved.
In summary, the setpoint knob changes
the working force by altering the
desired setpoint voltage. This results in
a different cantilever deflection in order
to have the reflected laser spot fall on a
different section of the PSD, and since
the cantilever constant is the same, the
total force changes with the change in
deflection. The bias knob changes the
working force by altering how much
force the setpoint voltage of 0 V
actually corresponds to. It does so by
adding or subtracting an offset to the
actual voltage out of the PSD circuitry.
Both are equally valid means of
selecting the working force, and each
user may have an individual preference
as to which method is advantageous in Figure 124
various situations.
Handshaking
One of the most versatile techniques included in the SPM 1000 system is the ability to perform
simple data acquisition by utilizing the TTL input and output available on the DT3016 board.
This is achieved by using the Handshake menu option in the spectroscopy mode that is
configured. The following discussion gives more details on the technique and provides some
specific examples of the sort of experiments that can be done.
The external equipment to be used must have
two characteristics. First it must provide an
external input that will start data acquisition
when a TTL input is set to a specific state. (A
simple case is some spectrometers that can be
turned on when a TTL input is moved to the
HIGH (+5 V) position.) It must also provide a
status line that it can change state that the
XPMPro TTL Input can detect. A TTL line that
the device places HIGH while acquiring data
then changes back to LOW when the
measurement is complete is sufficient.
Figure 125 represents a simple TTL
handshaking scheme. At some time prior to
point t1, the tip has been moved to the proper
pixel and all input channels to be imaged have
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been read by the ADC board. The TTL output channel is then changed to the HI level. The
external equipment recognizes the voltage applied to its input has changed and interprets this as
the trigger to commence data acquisition. At some time later, (the delay between A and B
depends on the equipment being used. For example, a laser may need some warmup time.) The
equipment changes its output voltage (dotted line) to a HI value (point t2) which XPMPro reads
on the TTL input channel and interprets this to hold the tip position because the external
equipment is in the process of taking data.
When the external data acquisition is
over, the status line on the equipment
is changed to its original value (point
t3). XPMPro reads this on the TTL
input channel and interprets this that
the external acquisition is finished.
The control electronics then will move
the tip to the next pixel and all
channels will be read to form images.
The external acquisition routine is then
repeated at every pixel.
On a Revision 8.5 SPM100, the TTL
connections are pin 9 (input) and pin
15(output) on the rear panel DIO
connector. When using an adapter box
with any SPM100 prior to version 8.5,
the TTL In and TTL Out are explicitly
Figure 126
labeled.
Handshaking is configured using the
window shown in Figure 126. The handshaking channel needs to be chosen for both the input
signal and output signal. Unless the DT335 TTL board is present, the only option that can be
used is User TTL Out and User TTL In for each parameter. If the DT335 board is present, this
adds extra TTL channels and one of them can be configured as the handshaking line if desired.
These are the ones designated Line A or B. The flexibility in the software allows one to define
the “start” signal sent to the equipment as either TTL HI or TTL LO. This is accomplished by
using the Active High and Active Low radio buttons contained in both the input and output
sections. To prevent a completely stuck acquisition it is a good idea to configure a timeout so the
software does not wait forever for a TTL signal that is not going to be returned. This is entered
in the Hardware Timeout parameter.
Lateral drift correction
XPMPro can automatically track a feature on the surface and correct for any drift due to thermal
or piezoelectric effects. A distinctive feature on the surface should be selected and after each
image acquisition, an area of the scan is searched for the same feature. If alternating slow scan is
ON, the pattern is matched every other scan frame (only for the images taken from top to
bottom). Small offsets are then applied by the DSP board in order to maintain the same relative
position within the scan frame. This means the feature will not appear to move over the surface
because the scan frame is shifted between each image. The size of the feature and also the size of
the search area can both be set to any value as long as the area does not fall outside the current
scan area using the window accessed via the Drift window(Figure 127) in the Settings menu. For
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example, if the search area is defined to be 35 pixels, then the center of the area cannot be within
18 pixels of any edge. Tracking is activated by clicking on the tracking icon within the
acquisition window.
The search area and feature size are both square in shape so the term radius is a bit of a
misnomer, but the size specified in the window is doubled to create the real feature size. The
value can be specified in physical units or pixels by utilizing the Incr in Pixels check box. The
Reference Radius is used to store the “core” feature which is ten compared to subsequent scans.
The Search Range is the section of the image where the stored feature is fit to each part and a
quality of fit calculated. The highest value is then determined to be the location of the original
feature.
If the surface is evolving over time and the
feature is changing its shape, it is better to
compare the feature appearance to the
previous image rather than the image when
first turned on. This can be more accurate as
the tracked feature changes from image to
image. To use this algorithm instead of
always comparing the feature at t=0, check
the box named Previous Reference Image
Drift.
XPMPro contains two types of drift
correction and the best choice for the
situation will depend on the scan head and
the environment. If a small shift should be Figure 127
applied after each image to recenter the
feature in the scan frame, then choose Send Offset for the type of correction. If the drift is
significant enough to skew the unit cell of a surface given the time it takes to acquire an image,
then Send Offset and Vector should be chosen. This will calculate the location of the feature
compared to the original location and divide the offset by the time to acquire an image and form
a vector with an x and y component. These vector components will be sent to the SPM100 scan
board and during the next frame, the raster will be modified to adjust its output on a line by line
basis in an attempt to keep up with the surface drifting below the tip. In an ideal world with
consistent drift over a lengthy time period, every subsequent scan will find the feature exactly in
its original location since the scan frame is adjusted to move at the same velocity as the feature.
However, in practical terms this is rarely the case. If there is an offset between the feature
location and the original location in the next frame, a new vector is calculated and this is then
placed in effect for the next frame. This continues until the drift correction is deactivated. If at
some point the correction is large enough that the scan frame bumps into the border of the
maximum reachable scan area (red box in the NAV window) then the vector correction is
disabled and only an offset correction is applied between scan frames.
When the tracking is turned on, the user will be asked to click on the area of the image where the
relevant feature is located. A small dark green box will then be drawn that represents the feature
to be searched for each time. The z values of this region are stored in memory. The larger bright
green box represents the area of the image that will be searched to locate the desired feature. If
the drift is so large that the feature moves outside the search box during the scan, the algorithm
will do its best to find the closest match and adjust the offsets accordingly. Care must be
exercised to make the search area large enough to assure the object will be found, but not so
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large that multiple features that are very similar in appearance are contained within the search
area. Also, increasing the search area will also increase the amount of time required to complete
the search. For a search area of approximately 40 pixels, the algorithm usually takes less than a
second to complete on a 1 Ghz Pentium 4 computer.
After each fit, a bright blue square is drawn on the real-time acquisition window (RTAW) where
the selected feature was found (Figure 128). In this particular test with a gold on mica sample, a
small protrusion from the terrace edge was selected and subsequently tracked. Since this feature
was supposed to be located where the aquamarine box is drawn, offsets are applied to the X and
Y scan signals to shift the frame the amount of separation between the aquamarine and bright
blue squares. This can be visualized in
the Scan Area window as the yellow
scan area box will move a small amount
and the next image will start. In the
subsequent frame, the two may not
perfectly overlie because additional drift
has occurred during the scan frame in
the time it takes to complete the scan
frame and perform the calculation.
An information bar is added to the
RTAW that provides the number of
images acquired since tracking was
activated (1) as well as the total distance
shifted along the X (-18.7 angstroms)
and Y (-81 angstroms) axes. The total
amount of time that tracking has been
active (1 minute 48 seconds) is also
displayed. This last piece of information
along with the total shift in the x and y
direction allows the actual lateral drift
rate to be calculated. If vector drift is
active two additional items are added to
the status bar, which are the components
of the vector currently in effect for the
scan.
Figure 128
When either drift correction algorithm is active, a log of the drift corrections is created in the
XPMPro folder. This file will begin with the string DriftLog and then have the rest of the name
formed by a uniquely generated string based on the date and time the drift correction was turned
on.
Vertical drift correction
The auxiliary feedback loop provided by the DSP board can be used with a long time constant as
a supplemental correction signal operating in parallel with the analog feedback loop provided by
the SPM 100. The DSP board can sample the topographic signal and output a voltage to
maintain a constant z value (usually zero). This can correct for slow drift effects due to thermal
expansion/contraction during variable temperature experiments. Connect a BNC from Z Position
monitor output to the DSP ADC #1. When activated, the signal is output from the DSP DAC and
summed into either Z Scan or Z Offset depending on which rear panel BNC is connected. If a
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separate piezo element is used for Z Scan and Z Offset, then usually it is advantageous to sum
the output of the auxiliary loop into Z Offset to allow more of the maximum output voltage
available to the z scan signal itself.
The advantage to utilizing the second feedback loop is increased resolution because the
correction is applied in hardware before the topography signal is sampled. The same argument
outlined in the SPM 100 manual concerning hardware slope compensation is applicable here. If
the drift is quite large, then to keep from saturating the ADC during the course of a single scan,
the ADC gain must be decreased,
which effectively decreases the
resolution. If the vertical surface
features are only 0.1 nm in extent, but
the total z drift is 200 nm during a
single image (for example while
heating or cooling the sample), the
ADC gain must be adjusted so the
dynamic range of the topographic
signal does not exceed 200 nm which
leads to a least significant bit of 0.03
angstroms. However, with the second
feedback loop slowly correcting for the
drifting absolute z value, the total
extent of z signal the ADC will see can
be decreased to ~0.1 nm because the
primary feedback loop will only be
following the atomic corrugation and
Figure 129
not the slow drift due to thermal
effects. Therefore, the effective
resolution can be increased by a factor of 2000.
The second loop is activated in the bottom of the NAV window by checking the box Enable
Aux Feedback. To configure the action of the loop, open the Settings dialog shown in Figure
129. The most common use of the loop is to null out the z drift as described above. In that case
the mode should be set to Z Offset Control and the calibration parameters will be filled in
automatically based on the z piezo factors. The important parameter is the polarity of the
feedback. If the loop is activated and the analog feedback meter does not move to the center of
its range to indicate the loop has moved the feedback output to the middle of its range, then the
polarity is probably wrong. In that case, change the checkbox Aux Feedback Z Offset Invert. For
the RHK series of UHV microscopes the correct setting of this parameter is to have the box
checked as shown in the Figure 129.
If the mode is changed to User Defined then the scale factors should be entered in the two
parameters Units/Input volt and Units/Output Volt. This determined how much the output signal
for change for a given change in the input signal. The units can be changed when in user defined
mode by entering the appropriate value in the Feedback Units box. This can help entering
meaningful values for the calibration factors.
Under certain conditions, the auxiliary feedback loop can actually distort the topography data
and cancel out real differences in height on the surface. To avoid this situation, the loop can be
disabled during imaging by checking the appropriate box. If it is important to always have the
auxiliary loop active (an interferometer feedback system is an example) then the loop can
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automatically be activated as soon as the program starts. Keep in mind once the loop is activated,
it will remain active inside the SPM100 unless the controller is turned off. So, the software can
be halted but the auxiliary loop as well as the main analog feedback loop will both continue
working.
Any other signal can be monitored while the auxiliary loop is active and corrective action taken
if a threshold condition is met. One action that can be taken is the rear panel Digital IO Pen
UP/Pen Down line can be switched high to notify the user the threshold has been exceeded. This
line can also be connected to something external so a safeguard action is produced in case
exceeding the threshold will cause an undesirable action. If an interferometer feedback system is
getting close to the edge of a fringe then the tip can be retracted to realign the feedback system
to ensure the tip is not damaged if the detector hops from one fringe to the next.
Once the loop is active the response time can be changed using the Time Constant parameter in
the NAV panel. Also, for user defined mode, the digital setpoint can be entered here and the loop
will output a correction signal necessary to maintain the input at ADC#1 to the requested
setpoint value.
Tip tracking of a feature
Brian Swartzentruber
pioneered a very nice
technique where the tip is
oscillated in a circle while
monitoring an input
channel. The gradient of
the input is calculated as
the tip orbits and small
Figure 130
offsets are applied to the
tip position to keep the
location at the top of a maximum or the lowest point of a minimum. XPMPro is capable of the
same technique because of the DSP board. The x and y output voltages have small oscillations
digitally added to them while an input signal is measured using the DSP ADC#1. To activate this
feature connect the channel to be monitored to the input and configure the parameters
appropriately for the system under study.
The parameter window is accessed through the Tip Tracking pane of the NAV window.
Whatever output channel has been connected to the DSP ADC #1 input should selected in the
Tracking Channel box. Once this is done the other parameters are then displayed in the proper
units. Object height specifies the expected change in the feature size if the tip moves away from
it. Negative values would indicate a hole that would cause the actual monitored value to increase
when coming out of the hole. Object width is used to set the orbiting radius and the period of
the oscillation is set by orbit rate. The bandwidth of the DSP loop monitoring the channel and
applying corrections is set by the tracking time constant. If there is a phase lag between the tip
location and the change in the signal, this should be entered in the correct place to the DSP board
knows to apply the corrections with respect to the real tip location based on the known delay
between measuring the difference and the tip position.
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Once the parameters are entered, the feature is configured and ready to use. Before activating it,
an image must be loaded into the NAV window from a saved SM4 file. This is required so a
history of the local surface topography is saved as well as an image of the feature where the tip
is placed. To activate the function click the Enable Tip Track box in the pane. Then click the
location to place the tip over a unique feature in the NAV window. The tip will move to this
position and start to orbit the location. The tip should follow the path of the tracked feature until
tracking is disabled again at a later time. When the tracking is turned off, the SM4 file is
automatically saved again with the X, Y
positions as a function of time added to the
file. To visualize this data on the image,
open the file in the DAW and right click on
the image. A new menu item will be present
named Show Tip Track. By clicking on this,
lines will be overlaid on the image showing
the tip path as a function of time. If multiple
data pages are in the image, only the one
that was loaded into the NAV window
before tip tracking is activated will be able
to have the path overlaid.
Forming a panorama view in the
NAV window
When a new image is loaded in the NAV
window, the old images are not erased. This
permits the overlaying of multiple images to
create a larger picture of the surface. The
entire red box could be filled with images,
each one taken over a small region and then
combined together. After loading the
window with many images, individual onces
Figure 131
can be deleted by clicking on the image and
choosing Clear. The selected image to be
cleared is indicated by a dashed line around the image perimeter. To remove all images, use the
Clear All button. An example of a large view is presented in Figure 131.
The large view can be permanently saved in a graphics
format by clicking the Export button in the window. A
file dialog will be opened prompting for a name and
format type. The entire visible region in the NAV window
is exported and blank areas are filled in with a white color.
The exported bitmap for the example shown is displayed
in Figure 132.
Manipulation and Lithography
XPMPro contains powerful lithography and atomic
manipulation tools. The tip can be moved to arbitrary
locations and an atom “grabbed” by altering the conditions
and then the tip can be moved to a new location and the
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atom “dropped”. This allows the building of complicated structures one atom at a time. When
completed, the area of the surface can then be imaged using the same tip in order to study the
electronics effects of the small structure on the surrounding region.
To understand the principle of the manipulation and lithography routines, it is important to
understand the meaning of the two terms used within the software. The two types of tip motion
are called drag and move. A “move” is performed by placing the mouse cursor in the NAV
window and clicking. The tip will move in a straight line directly to the clicked location at a
predetermined speed. Conditions can be changed during motion which can be used to induce a
feature on the surface if desired. A “move” is usually used to pick the “pen” up and start drawing
a new line without inducing a feature on the surface that would connect them. It is also used
during manipulation to place the tip over the next atom to be dragged into position. A “drag” is
performed by placing the mouse cursor
over the tip icon and clicking the left
mouse button to “grab” the tip. As long
as the mouse button remains pressed the
tip will follow the mouse cursor at a
predetermined speed. Unless the mouse
cursor is moved rather slowly, the tip
will probably fall behind the cursor
location since moving the tip too fast
can crash it into the surface due to the
relatively slow response of a feedback
loop. The software periodically reads
the mouse cursor location and send the
location to the DSP board. When this
occurs the tip will change direction and
start moving towards the new point.
This means the tip will not exactly
follow the path the mouse cursor
follows unless the mouse is moved
quite slowly to make sure the tip stays
Figure 133.
with it. An example of this behavior is
illustrated in Figure 133. The drag
speed was set to a relatively slow value. The purple line represents the mouse cursor path and the
light blue line represents the actual tip path. The most dramatic difference is when drawing the
circle in the lower left corner. The first half of the circle was drawn while slowly moving the
mouse so the tip kept up to the location. The second half of the circle was drawn very quickly
such that the next time the software measured the mouse location and sent the destination to the
DSP board, the circle was done but the tip had not moved far. Therefore the tip was instructed to
move directly to the end of the circle and it took the shortest possible path and went straight
across the inside of the circle to the endpoint of the mouse path. Also, as mentioned earlier the
color of these lines can be redefined by right clicking in the window and choosing the Drawing
Colors submenu.
As can be seen from the diagram, very complex shapes can be drawn and the tip will trace out
the shape as long as the mouse cursor is moved slowly and the tip is permitted time to catch up
to the mouse as the path is drawn.
Actual lithography takes place when some condition is changed during tip motion. This
condition induces a feature to be created under the tip. Examples include a brute force method of
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pushing an AFM tip into a self assembled monolayer to “plow” the material out of the way, or
applying a bias to a coated cantilever on a silicon surface in the presence of a water meniscus.
The conditions are defined using the window opened from the Manipulation button on the right
side of the main area.
There are two tabs in the window
related to manipulation and
lithography. The first one is used to
determine the conditions during
motion and the second one sets the
scale factors and physical units of the
applied conditions for ease of use.
Different speeds can be specified for
the two motions. Be careful to not use
an excessive setting for a given
feedback bandwidth or the tip may
not follow the surface and could be
damaged by tip-sample contact. Also,
what may be appropriate one day may
not work well on another day due to
the changing feedback settings that
often are required. When changing
conditions to induce features on the
Figure 134
surface, it is important to use a
velocity that allows time for the
reaction to take place so the feature is drawn. When dragging an atom to another location, a high
speed could cause the tip to lose the atom and leave it behind. Some experimentation will be
required to determine optimal conditions. A delay can also be entered to allow the system time
to equilibrate before actually commencing motion.
During motion there can be no conditions changed, one condition changed, or two conditions
changed. Additionally, the two conditions can be pre-programmed and saved so enabling or
disabling them is as simple as checking a box instead of needing to set the levels back to zero to
disable them which is inconvenient. The lower section of the Move tab serves two purposes, the
condition can be turned on or off during motion and the signal level applied during the motion
can be defined here. To have a defined condition apply during a motion, place a check in Enable
box and enter the Move Level or Drag Level so the condition is active during that motion. For
example, to have the bias modulated at two different levels during the move and drag operation,
both check boxes in the column would be marked and the levels then defined underneath each
box. To have the bias modulated only during a drag, the enable box for the move action would
be left unchecked and only the drag checkbox marked.
The output channels can have meaningful labels and units given by entering the desired
parameters in the Define tab shown in Figure 137. The two outputs can have names given so it is
easier to understand what signal the DAC will be changing during the motion. The appropriate
label is determined by the connection between the DAC and the equipment. In the example
shown in the figure, the first DAC is connected to a SPM100 rear panel bias modulation input
and the second one is connected to the SPM100 rear panel Set point input. However, the DACs
can change any signal during the motion so the arbitrary name should be changed to reflect the
signal to be affected. For example, if the DAC is tied to a magnetic field controller to alter the
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field while the tip moves, the name could be “B field”. Whatever physical signal is changing, the
correct units should also be entered so the signal level can be specified in meaningful units. A
calibration factor also needs to be entered in order for the software to properly output the correct
voltage level that will have the requested end effect on the signal to be modified. An offset can
also be applied to the signal different from the specified move and drag level in the previous tab.
The output channel should be selected with the next parameter; any of the four DACs can be
used. However, keep in mind that the A and B pair of outputs are multiplexed. Therefore if two
signals are to be changed simultaneously during motion, one of the outputs will need to be either
1A or 1B and the other one must be 2A or 2B. If one of the signals is going to alter the STM bias
between the tip and the sample, then STM Bias Mode should be checked so the software will
measure the bias due to the knob and output a DAC voltage necessary to reach the requested tipsample bias.
When moving atoms around the surface it is advantageous to acquire a small image scan after
dropping the atom in its desired position. The image will immediately show if the object is in the
correct place. If the image shows no feature then it was accidentally dropped somewhere along
the way. The capability to acquire a small image is present in XPMPro. The image is defined in
the Atomic Manipulation tab as shown in Figure 135. The size of the small image should be
defined and the channel to acquire. For better sensitivity the ADC Range can also be changed
similar to the gain specified in the Scan/Input tab but keep in mind this gain is applicable only
for the small image taken when an atom is dropped after a Drag operation. The speed of the scan
can be defined in the next section. By default it is acquired with the same conditions of the last
image acquired which means the feedback loop will reliably follow the surface and not damage
the tip. If an independent speed is desired, use the other radio button and then enter an
appropriate speed. Be careful to not make
this too fast for the feedback loop settings
or tip damage may occur.
When the image is acquired, it is in the
region of the tip location when motion
ends. If the feature is not there usually the
operator will back track the path and
acquire images along the way looking for
the atom. Instead of forming small images,
a rectangular image can be formed by
scanning on either side of the entire path
the tip followed. Wherever it was dropped,
it will appear in the acquired image. Then,
the tip can be relocated to this position and
the atom picked up again and dragged to
the intended position. To activate this
automatic image acquisition during tip
Figure 135
move/drag operations mark the Atomic
Manipulation check box directly below the
Move/Drag radio button in the Mouse action section. The
acquired image is overlaid in the NAV window image area. Figure 136: Atomic manipulation
An example of manipulation demonstration is shown in Figure 136.
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Figure 137
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SM4 Data File Format
This is the “SM4” file format as of March 18, 2008. You can convert sm2 files, having file
header starting with “STiMage 3.1”, to SM4 files using the converter given in the DAW menu.
The SM4 file starts with a File Header which contains general information about the file format
version and offsets to the beginning of each page array as well as the PRM file and the image
thumbnails.
File Header
File Header Size
Stores the size of structure SfileHeader. This size could be used to read the SfileHeader
structure, so in the future if any new fields are added to this structure it will not affect the
existing file.
Struct SfileHeader
{
Signature: “STiMage 005.000 1”
Major version: 005
Minor version: 000
Unicode:
1
Total Page count: (4 bytes) Stores the total pages saved in the file
Object list count : (4 bytes) Stores the count of Object stored in file header
Object field size: (4 bytes) size of SrhkObject structure = 12
Reserved [2]: (8 bytes) 2 fields reserved for future use
}
Object List : Stores the file header objects. Currently we are storing:
1. Page Index Header
2. PRM Data
3. PRM Header
Any objects can be added to this list in future.
An Object contains the Object ID, the data offset and its size. Using the data offset and
size, we can read the corresponding object data.
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Struct SObject
{
Object ID: (4 bytes) – Type of data stored
Offset: (4 bytes) Data offset
Size: (4 bytes) size of the data
}
Defined Object Ids:
Undefined
-0
Page Index Header - 1
Page Index Array
-2
Page Header
-3
Page Data
-4
Image Drift Header - 5
Image Drift
-6
Spec Drift Header
-7
Spec Drift Data (with X,Y coordinates)
-8
Color Info
-9
String data
- 10
Tip Track Header
- 11
Tip Track Data
- 12
PRM
- 13
Thumbnail
- 14 //Not implemented
PRM Header
- 15
Thumbnail Header - 16
The basic unit in a file is a “page”. A page can be a single image, a single spectrum, or a group
of spectra. One file may have many pages, including combinations of image and spectral data.
Each page starts with a header to provide the information about the page layout within the file as
well as an array to point to each page.
Page Index Header
The page index header stores the details of page index array, which contains the array of
page offsets and other info. Using the Index array we can locate the required page data,
thumbnail data for the respective page, etc without reading the entire SM4 file.
Page count:
(Data type long)
Bytes used 8 bytes
Stores the number of pages in the page index array
Object List Count:
Stores the count of objects stored after page index header
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Reserved [2] : (8 bytes)
Two fields reserved for future use
Object List:
Stores the Index header objects. Currently we are storing one object:
1. Page Index Array:
Page Index Array
Based on the page count, an array of SPageIndex structure will be stored after the Page
Index header.
Struct SPageIndex
{
Page ID: Unique ID for each Page
Page Data Type: The type of data stored with the page. Defined types are.
0 = image data
1 = line/spectral data
2 = xy_data
3 = annotated line/spectral data (see note below)
4 = text_data
5 = text_annotate
6 = Sequential_data
Page Source Type: Identifies the page source type. The defined types are given below
0 = raw page
1 = processed page
2 = calculated page
3 = imported page
Object List Count: Stores the count of Objects stored after each the Page Index
Minor Version: (4 bytes) stores the minor version of the file (minor version = 0)
}
Object List: Stores the Page Index objects. Currently we are storing:
1. Page Header
2. Page Data
3. Thumbnail
4. Thumbnail header
After this begins a page of data. Here is a simple diagram that outlines the layout of each page of
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data.
Page Header
The description about the parameters, bytes used and data type are given below.
Field Size
Data type: short
Bytes used: 2 Bytes
Total size of page parameters excluding strings and Field Count itself (FIELD_SIZE =
170 as of this version).
Each page starts with a variable of type short, which gives you the size of the page
structure. Decrease the size by 2 and by reading that much byte from the file gives you
the following parameters about that page.
Signature
Data type: WCHAR []
Bytes used: 36 Bytes
Signature is used to identify the version of the page. Version format is as shown below.
To store version, eighteen characters are used (including null character) and characters
are in the Unicode format.
“STiMage 004.002 1” where STiMage 004.002 gives you the version and and right most
value “1” indicates that file is in Unicode format. For non-Unicode files it will be zero.
String Count
Data type: short
Type
Data type: int
Bytes used: 2 Bytes
This variable gives you the number of strings in the page.
Bytes used: 4 Bytes
The type of data stored with the page. Six types are supported.
0 = image data
1 = line/spectral data
2 = xy_data
3 = annotated line/spectral data
4 = text_data
5 = text_annotate
Page type
Data type: int
Bytes used: 4 Bytes
Identifies what kind of data an image page represents. The possible types are:
0 = undefined
1 = topographic image
2 = current image
3 = aux image
4 = force image
5 = signal image
6 = image FFT transform
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7 = noise power spectrum
8 = line test
9 = oscilloscope
10 = IV spectra
11 = image IV 4x4
12 = image IV 8x8
13 = image IV 16x16
14 = image IV 32x32
15 = image IV center
16 = image interactive spectra
17 = autocorrelation page
18 = IZ spectra
19 = 4 gain topography
20 = 8 gain topography
21 = 4 gain current
22 = 8 gain current
23 = image IV 64x64
24 = autocorrelation spectrum
25 = counter data (usually NSOM)
26 = multichannel analyzer data (usually NSOM)
27 = AFM data using RHK AFM-100
28 = CITS
29 = GPIB
//not used at present
30 = Video channel (Ivideo)
//not used at present
31 = Image out spectra (Ioutspec)
32 = Idatalog
//not used at present
33 = I_Ecset
//not used at present
34 = I_Ecdata
//not used at present
35 = I_DSP_AD
DSP channel //not used at present
36 = Discrete Spectroscopy (Present Position) (struct member:IdiscSpecData)
37 = Image + Discrete Spectroscopy (struct member:IimageDiscSpecData)
38 = Ramp Spectroscopy (Relative points) ((struct member:IivpointSpecCoord)
39 = Discrete Spectroscopy(Relative points) ((struct member:
IivDiscSpecDataSpecCoord)
Data Sub Source
Data type: int
Line Type
Data type: int
Bytes used: 4 Bytes
This parameter provides additional information on the stored data page.
Bytes used: 4 Bytes
Identifies what kind of data is represented by a line or spectral page. The recognized
types are given below.
0 = not a line
1 = histogram
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2 = cross section
3 = line test
4 = oscilloscope
5 = reserved
6 = noise power spectrum
7 = I-V spectrum
8 = I-Z spectrum
9 = image X average
10 = image Y average
11 = noise autocorrelation spectrum
12 = multichannel analyzer data
13 = renormalized IV data from variable gap IV
14 = image histogram spectra
15 = image cross section
16 = image average
17 = Image Cross Section (Gsection_fdata)
18 = Image Out Spectra (Goutspec)
19 = Datalog Spectrum (Gdatalog) //Not used at present
20 = Gxy
//Not used at present
21 = Electro chemistry (Gechem)
//Not used at present
22 = Discrete Spectroscopy. (Gdiscspec_data)
X,Y Coordinates Width and Height Data type: structure RECT_SIZE Bytes used: 16
Bytes
typedef struct tagRECT_SIZE
{
int m_nX;
// X corner
int m_nY;
// Y corner
int m_nWidth;
// Width
int m_nHeight;
// Height
} RECT_SIZE;
m_nWidth: The number of pixels or points in the X direction for an image page, or the
number of points per spectra/line for line pages.
m_nHeight: The number of pixels or points in the Y direction for an image page, or the
number of spectra stored in the page
Source Type
Data type: int
Bytes used: 4 Bytes
Identifies the page source type. The recognized types are given below
0 = raw page
1 = processed page
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2 = calculated page
3 = imported page
Image Type
Data type: int
Scan
Data type: int
Bytes used: 4 Bytes
Identifies what kind of data is represented by an image
0 = normal image
1 = autocorrelation image
Bytes used: 4 Bytes
The scan direction (direction of data acquisition) in an image. It is not meaningful for an
I-V curve, for example. On the computer screen X is horizontal and Y is vertical.
0 = right
1 = left
2 = up
3 = down
Group ID
Data type: int
Page Data Size
Data type: unsigned long
Bytes used: 4 Bytes
An Integer value to identify the pages acquired during an acquisition. All the pages
acquired during an acquisition will get the same group id.
Bytes used: 4 Bytes
The total number of data bytes in the data section. It is equal to m_nWidth * m_nHeight*
sizeof (long int). For Float data it should be m_nWidth * m_nHeight* sizeof (float). In
case of Disc. Spectroscopy, the datasize = ((m_nWidth * m_nHeight ) + m_nWidth) *
size of (float). Additional size of width is to store the user enterd voltage values for a
page.
Page will have float data if the Line Type is any one of the following:
Gdatalog, Gechem, Givnorm, Gfft_power, Gautocorr, Goutspec
Gdiscspec_data, Ghistogram, Gx_ave,Gy_ave
All image data is stored as 32 bit signed integers. Most spectral data is either 32 bit
signed integers or floating point such as power spectra and autocorrelation spectra point.
Minimum Z Value
Data type: Unsigned long
Maximum Z Value
Data type: Unsigned long
Stores
Bytes used: 4 Bytes
the minimum Z Value.
Bytes used: 4 Bytes
Stores the Maximum Z Value.
X Scale, Y Scale, Z Scale Data type: float
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The X, Y, Z physical units per pixel or bit.
X Y Scale
Data type: float
X Offset
Y Offset
Z Offset
Data type: float
Period
Data type: float
Bias
Data type: float
Bytes used: 4 Bytes
This is the change in X in physical units per Y line. This is used for drift Correction and
is 0 for newly acquired images.
Bytes used: 4 Bytes each
The origin of the X value, or the X coord of the image center. The physical unit is '
XOffset ' + 'XScale ' * (x number) The Y and Z offset are similar.
Z is the acquired data. X and Y are the image coordinates for 3D data. 2D data is plotted
as X-Z. The Y coordinate is just an index. For an I-V curve, for example, if 4 curves are
acquired, X is in Volts, Z in Amps and Y is 0, 1, 2 or 3. In a force image X and Y are
meters and Z is Newton.
Bytes used: 4 Bytes
The time to acquire each data point.
Bytes used: 4 Bytes
The sample bias in volts (not relevant for most AFM data)
Current
Data type: float
Bytes used: 4 Bytes
The absolute value of the sample current in amps (not relevant for most AFM data)
Angle
Data type: float
Bytes used: 4 Bytes
The angle by which the image is rotated. (Normally 0)
ColorInfoList Count
Data type: int
Bytes used: 4 Bytes
Stores the number of color info.
Grid X Size
Data type: int
Bytes used: 4 Bytes
Spectral grid X size
Grid Y Size
Data type: int
Bytes used: 4 Bytes
Spectral grid Y size
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Object list count
Stores the count of Objects stored after the Page Header
Reserved [16]:
(16 * 4 bytes = 64) Reserved for future use
Object list:
Stores the Page header objects, Currently we are storing
1. String Data
2. Image Drift header
3. Image Drift Data
4. Spec Drift Header
5. Spectral Data
6. Color Info
7. Tip-track Info Header
8. Tip-track Data
TEXT STRINGS
StringCnt gives you the number of strings in the current page. Each string is written to
file by first writing the string length, then the string. So when you read, first read a short
value, which gives you the string length, then read that much bytes which represents the
string.
strLabel: String that goes on the top of the plot window, like “Current Image”.
strSystemText: A comment describing the data.
strSessionText: General session comments.
strUserText: User comments.
strPath: Path and name of the SM4 file, which holds the page.
strDate: Stores the date at which data is acquired.
strTime: Stores the time at which data is acquired.
strXUnits: Physical units of that axis, like “m” or “A”.
strYUnits: Physical units of that axis.
strZUnits: Physical units of that axis.
strXLabel.
strYLabel.
strStatusChannelText: Status channel text
strCompletedLineCount: Completed line count info. This string contains the last saved
line count for an image data page. For all other pages, this value will be zero.
StrOverSamplingCount: This string contains the Oversampling count for image data
pages. For all other pages this value will be zero.
StrSlicedVoltage : The voltage at which the sliced image is created from the spectra
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page. This string will be empty for pages other than sliced image pages.
StrPLLProStatus : This string contains the PLLPro status text, if the operating mode is
selected as PLLPro master or PLLPro user.
Page Header – Sequential Data Page
The sequential data page is generic page in which the page data is a (m,n) array. Where
‘m’ is the number of parameters in the array and ‘n’ is the array count. The array
elements will be all float type. The parameter info is stored in the page header.
(Sequential Data Header).
If the PageDataType is Sequential_data, then Page header contains the following
parameters.
Data Type
Data Type: int
Bytes used:(4 Bytes)
Type of the Data stored in the page. The defined types are
1 = Spec Drift (Stores the SSpecInfo structure as the Data, Param Count gives the
number of float data in this structure.)
2 = Image Drift (Stores the SImageDrift structure as the Data, Param Count gives the
number of float data in this structure.)
3 = Tip Track (Stores the StipTrackInfo structure as the Data, Param Count gives the
number of float data in this structure.)
Data Length
Data Type: int
Bytes used: (4 Bytes)
Stores the Array Size
Param Count
Data Type: int
Bytes used: (4 Bytes)
Number of parameters (float data ) in an array element
Object List Count
Data Type : unsigned int
Bytes used: (4 Bytes)
Count of objects stored after the header
Data Info Size
Data Type : unsigned int
Bytes used: (4 Bytes)
Size of the SXdataInfo structure – excluding the string
Data Info String Count Data Type : unsigned int
Bytes used: (4 Bytes)
Number of strings in the SXdataInfo structure
Object List
List of object stored after the sequential data header. Currently we are storing
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1. Image Drift Header
2. Spec Drift Header
3. Tip Track header
struct StipTrackInfoHeader
{
FILETIME m_ftStartTime;
float m_fFeatureHeight;
float m_fFeatureWidth;
float m_fTimeConstant;
float m_fCycleRate;
float m_fPhaseLag;
unsigned int m_unStringCount;
unsigned int m_unTipTrackInfoCount; //Stores the array size of the StipTrackInfo
rhk_string m_szChannel;
} STipTrackInfoHeader;
struct StipTrackInfo //Array of this structure will be stored in the tip-track data
{
float m_fCumulativeTime;
float m_fTime;
float m_fdX;
float m_fdY;
}STipTrackInfo;
Data Info
An array of Data Info is stored after the page header object list. It contains the
information about each parameter stored in the page data. The following are the
parameters in this structure
1. Param gain : Data Type float
Bytes used: (4 bytes)
2. StrLabel: (Data Type : string, the string size will be written before the string (2
bytes))
Name of the parameter
3. strUnit: ( Data Type : string)
Unit of the Parameter
The above details will be repeated for ‘n’ time where n is the ‘Param Count’
PAGE DATA
Page Data size and file Offset can be obtained from the Page data Object Stored in the
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Page Index array. Reading that much data from file gives you the acquired data. If the
Line Type is Gdatalog / Gechem / Givnorm / Gfft_power/ Gautocorr / Goutspec/
Gdiscspec_data /Ghistogram /Gx_ave /Gy_ave OR if the Page Data Type is
Sequential_data then the data is of type float otherwise data type is long int.
SPECTRAL DATA
If Type is line/spectral data and the Page Type is either image interactive spectra (type
16) or ramp spectroscopy (type 38) or image+discrete spectroscopy (type 37) or
discrete spectroscopy (type 39) then Spec Drift header and an array SSpecInfo is stored
after the page data. The data offset and the size of structure (SSpecDriftHeader and
SspecInfo) is stored in the Spec Drift Header and Spectral Data Object respectively in the
Page header object list. m_nHeight in the Page header gives the array size. If
spectroscopy drift correction is disabled then the drift info is filled with default values.
Struct SSpecDriftHeader
{
FILETIME m_ftStartTime; - Start time
int m_nDriftOption; - 0 = disabled, 1= each spectra, 2 = each location
unsigned int m_unStringCount; - number of string parameter in this structure
rhk_string m_szChannel; - drift channel name
}
Struct SSpecDrift
{
float
float
float
float
float
float
float
m_fTime;
m_fXCoord;
m_fYCoord;
m_fdX;
m_fdY;
m_fCumulativedX;
m_fCumulativedY;
}
READING COLOR INFO
If the Page Type is image_data, then the next short value gives you the total size of the
fields you have to read for color information Otherwise it is the start of the next page.
If the PageType is image_data, then the next short value gives you the size of structure
SColorInfo (Display related data) and we have to read that structure that is used for
display related things. ColorInfoList Count gives the size of ColorInfo list. The Structure
is given below
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typedef struct tagsColorInfo
{
short
m_nStructSize;
sHSVColor m_sHSVStart;
sHSVColor m_HSVEnd;
int
m_nClrDirection;
int
m_nNumEntries;
float
m_fStartSlidePos;
float
m_fEndSlidePos;
SColorTransform
m_sTranform;
} SColorInfo;
typedef struct tagsHSVColor
{
float m_fH;
float m_fS;
float m_fV;
}sHSVColor;
struct SColorTransform
{
FLOAT m_fGamma;
FLOAT m_fAlpha;
FLOAT m_fXStart;
FLOAT m_fXStop;
FLOAT m_fYStart;
FLOAT m_fYStop;
INT
m_nMappingMode;
BOOL m_bInvert;
}
Drift Data
If the Page Data Type is image_data, then the image drift header and image drift is
stored after the color info list. If the drift is disabled, then this structure will be filled with
default values. The offset and structure size is stored in the Image drift header and Image
Drift data objects respectively.
Image Drift header
Struct SimageDriftHeader
{
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FILETIME m_ftStartTime; - Image start time
int m_nDriftOption; - 0 = disbled, 1 = enabled, 2= vector drift enabled
}
Image Drift
The following are the structure elements:
SImageDrift
{
float m_fTime;
float m_fdX;
float m_fdY;
float m_fCumulativedX;
float m_fCumulativedY;
float m_fXRate; //Vector drift X Rate
float m_fYRate; //Vector Drift Y Rate
}
Tip-track Data
Tip-Track header and Tip Track data
During Tip-Track, the track details are stored into the loaded image in NAV. An array of
StipTrackInfo structure is stored as the track-data.
STipTrackInfoHeader.m_unTipTrackInfoCount gives the number of elements in the
STipTrackInfo array. For structure details STipTrackInfoHeader and STipTrackInfo
The offset and size is of the structures is saved in the Page Header Objects Tip Track
Header and Tip Track Data respectively.
PRM Data
PRM Data used for the current acquisition is stored into the SM4 in compressed format.
PRM header and PRM data are written after writing all of the page data. The PRM
header contains the following members. We are using Zlib for the data compression.
SPRMHeader
{
int m_nCompressionFlag; //0 = Not compressed, 1==Compressed
long m_lDataSize; //Original Data size (Before compression), used for
//decompression
long m_lCompressionSize; //Compressed buffer size
}
The user has the option to select the PRM data stored in the SM4 file. While selecting the
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PRM data from SM4, it will be saved into the application path with the SM4 filename.
Thumbnail Header and Thumbnail Data
In a DAW, instead of reading the entire page data to display the thumbnail, we are
storing the reduced page data as thumbnail data for each page in SM4 file. The thumbnail
data size is stored in the thumbnail header. The offset and size of the thumbnail header
and data is stored in the Page index objects Thumbnail header (page type= 17) and
Thumbnail (page type= 15) respectively. Using this offset we can locate the thumbnail
data in Sm4.
For an image page, if the scan resolution (X or Y) is more than 128 then the page data is
averaged and reduced to Min (128, X Size) and Min (128, Y Size) pixels and is stored as
thumbnail data.
For a graph page, the curve average is stored as the thumbnail data.
The Width (X Size) and Height (Y Size) is stored inside the thumbnail header.
SThumbnailHeader
{
int m_nWidth;
int m_nHeight;
int m_nFormat;
}
//Points per line
//Lines per frame
//=0 Raw data
The format represents the thumbnail data format. Currently, we are supporting only raw
data. In DAW, if the thumbnail data is present, then it reads the thumbnail data and
display (Page data will not be read in this case). If thumbnail data is not present, then it
reads page data and display.
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DSP Scan Board Commands
The DSP-based scan board can be controlled without the use of SPM32. Any computer on the
network can send and receive information to the scan board if the IP address of the board is
known. Auxiliary programs to ease this will be included in future software distributions.
Here are the list of valid commands that the scan board can interpret at this time.
float means 32 bit floating point. u32 means 32 bit unsigned integer. Do not do any big/little
endian conversion, the network chips take care of that.
Command code:
IGNORE_SWITCH
Command name in Litho files: is
Number of parameters to send: 1
Parameters:
u32 which
Examples:
ignore speed front panel switch: is 1
consider speed front panel switch: is 0
Notes:
As soon as the speed gets set once by the control computer, the front panel line time and line
time multiplier switch no longer control the scan motion speed. However the switch settings can
be read at any time by the control computer using the GET_STATUS command
Command code:
WRITE_Z_DAC
Command name in Litho files: wzdac
Number of parameters to send: 1
Parameters:
float output_voltage
Notes:
This command sets the output voltage of the Z DAC on the scan board. The parameter
output_voltage is clipped at ±10 V.
Command code:
SET_Z_SCALE
Command name in Litho files: szs
Number of parameters to send: 1
Parameters:
float Z_Sensitivity
Notes:
This command define the meaning of the physical units for the parameter of WRITE_Z_DAC
and for the Z sweep function s. Z_sensitivity is a sensitivity with the unit
[PhyUnit/DAC_output_Volt]
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Command code:
Z_SET_SPEED
Command name in Litho files: zss
Number of parameters to send: 1
Parameters:
float Z_Sweep_Speed
Notes:
This command sets the sweep speed for Z DAC sweeps. The unit of Z_Speed is [Physunits per
second].
Command code:
ABORT_Z_SWEEP
Command name in Litho files: abortz
Number of parameters to send: 0
Notes:
This command aborts a running Z sweep.
Command code:
SWEEP_Z_ABSOLUTE
Command name in Litho files: sza
Number of parameters to send: 1
Parameters:
float Z_Destination
Notes:
This command sweeps the ZDAC output to the Z_Destination value. The sweep parameters are
defined by the SETUP_Z_SWEEP command. The Z_Destination value has to be given in
Physical Units as they were defined by the SET_Z_SCALE command.
Command code:
SETUP_Z_SWEEP
Command name in Litho files: setupz
Number of parameters to send: 10
Parameters:
u32 Z_Sweep_Flags
u32 #Sample_groups
u32 #samples_per_group
u32 ThresholdMode
u32 AD_Channels
float Z_Sweep_Speed
float PreSampleDelay
float TimePerSample
float UpperThresholdValue
float LowerThresholdValue
Notes:
This command sets the control parameters for all subsequent Z sweeps. It also initializes the A/D
subsystem on the scan board to take data if any channels are set up in the AD_Channels
parameter. The parameters mean:
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Z_Sweep_Flags:
This is a set of flags that affect the operation of
the Z sweep and the way the Z sweep setup
works. The meaning of the bits is:
Bit 0: DSP Opens Feedback
0=No, 1=Yes
Bit 1: Reconfig DSP ADC
0=No, 1=Yes
The DSP Opens Feedback is not implemented in
versions <= 0x2c and requires a Revision 3 DSP scan
board. The Reconfig DSP ADC tells whether this
command should reset and re-configure the DSP A/D
buffers. If set the data buffers will be emptied. If cleared
previous data is held in the buffers. Note that
AD_Channels can still be changed from previous data
acquisitions without this bit set.
Sample_groups
This tells at how many positions along the line samples will be taken.
Please note that the begin and the end positions of the sweep are sample
positions. If you don't want A/D conversions taken during Z sweeps set
this parameter to zero. Zero is the default value for this.
u32 #samples_per_group
This tells how many triggers get issued to the SPM1000 data acquisition
board at each sample position. This trigger is also available on pin 3 of the
DB15 connector of the STM100/VSCAN100. In order to use these
triggers to take samples on the two ADCs on the board you need to
connect this pin 3 to pin 6 of the same connector.
u32 ThresholdMode
A value different from 0 in this parameter will cause the sweep to stop
when the A/D on the selected scan board A/D channels exceeds one of the
values specified in the ThresholdValue parameter. When bit 0 of this
parameter is set channel ADC1 will be used to compare to the threshold
values. When bit 1 is set channel ADC2 will be used. The channels will
only be used when data is taken on them during Z sweeps. When bits 0
and 1 are both set and data is measured on both channels only channel
ADC 1 is used. Besides that bit 4 of this value tells whether the ADC
values decrease (bit 4 is TRUE) or increase (bit 4 is FALSE) with
increasing DAC output voltage.
u32 AD_Channels
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This parameter tells which A/D channels on the DSP scan should get
sampled during all subsequent Z sweeps. A 1 means only A/D1, a 2 means
only channel A/D2 and a three means both channels.
float Z_Sweep_Speed
This sets the Z sweep speed in Physunits/s. The PhysUnit is defined by the
SET_Z_SCALE command. The speed gets internally adjusted to match
other internal parameters like resolution and maximum DAC update
speed. The DSP scan board also takes care that the time between sample
positions is bigger than TimePerSample in order to prevent A/D
conversion errors.
float PreSampleDelay
This number defines a delay time that the DSP scanner waits at each
sample position before the trigger sequence is started. The time is given in
seconds.
float TimePerSample
This parameter gives the time separation between two samples in the
trigger group at each sample position. The user has to make sure that this
time is not smaller than the conversion time of the A/D converters used.
float UpperThresholdValue
This gives the upper Threshold Value for the ThresholdMode. When the
ADC specified in AD_Channels reads a value that exceeds this the Z
sweep output will not be increased beyond that DAC value. Please note
that for this to work bit 4 in the AD_Channels parameter of this command
has to be set correctly
float LowerThresholdValue
This gives the Threshold Value for the ThresholdMode for up sweeps.
Command code:
BSET_DIO
Command name in Litho files: dioset
Number of parameters to send: 1
Parameters:
u32 bit_pattern_to_be_set
Notes:
All bits that are ONE in bit_pattern_to_be_set will be set in the DIO port of the scan board. The
bits are:
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DIO_PAGE
PAGE signal for SPM100 electronics, not
connected at this moment...
DIO_LOOP_INVERT
LOOP INVERT signal for the SPM100
electronics, not connected at this moment...
DIO_Z_RETRACT
Z_RETRACT signal for the SPM100
electronics, not connected at this moment...
DIO_HOLD_INT
HOLD_INT signal for the SPM100 electronics,
not connected at this moment...
SCANNING_LED
"Scanning" - LED on the front of the SPM100
ADC_CONV_START
This starts the conversion of the 2 scan board
ADCs
OVERRIDE_LED
"Override" LED on front of the unit
The coding of these values is defined in commands.h
Command code:
BCLR_DIO
Command name in Litho files: dioclr
Number of parameters to send: 1
Parameters:
u32 bit_pattern_to_be_cleared
Notes:
All bits that are ONE in bit_pattern_to_be_cleared will be cleared in the DIO port. See
description of BSET_DIO for the bit functions.
Command code:
TAKE_DIO
Command name in Litho files: diotake
Number of parameters to send: 1
Parameters:
u32 bit_pattern_to_be_taken
Notes:
All bits that are ONE in bit_pattern_to_be_taken will be made output bits so that the scan board
can control them. Either the scan board or SPM32 can control the bits. Please remember to set
the control back to SPM32 for all bits. Otherwise SPM32 will not work correctly. This function
requires a revision number of 3 and a kernel revision number of 1.4 to work. Please contact
[email protected] for details of a scan board upgrade.
Command code:
TRIGGER_ADC
Command name in Litho files: trigadc
Number of parameters to send: 0
Notes:
This triggers an A/D conversion on the two ADCs on the board. Use READ_ADC_BUF to get
the values. 15 data pairs of the two ADCs can be stored in a buffer on the board.
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Command code:
READ_ADC_BUF
Command name in Litho files: gadc
Number of parameters to send: 0
Notes:
This command reads the on-board A/D conversion buffers. The A/D conversions can be
triggered via the external trigger input as well as via TRIGGER_ADC command. The data for
the first 15 trigger events after a READ_ADC_BUF are stored in the buffer. This command
uploads the data in the buffer and then empties it.
Command code:
WRITE_ADC_BUF
Command name in Litho files: wadc
Number of parameters to send: variable
Notes:
This command writes "how_many" data points into the on-board A/D conversion buffers as if
they were written by the Data Acquisition. The first u32 word in the reply is the number of A/D
samples that get sent down to the board. This command is intended for testing and for writing
the output data for the replay mode
Command code:
GET GAINS
Command name in Litho files:
gg
Number of parameters to send:
0
Note:
This command returns a table that contains the high voltage gain parameters that are burned into the chassis
EEPROM of the SPM100 units. Please note that a reading of 6553.5 indicates that the EEPROM does not contain
the correct header revision. In this case the information might be in the modifications field of the EEPROM header.
The data structure returned by the GET GAINS command looks like this:
[0] u32 the GET_GAINS command code
[1] float X Offset Gain
[2] float X Scan Gain
[3] float Y Offset Gain
[4] float Y Scan Gain
[5] float Z Offset Gain
[6] float Z Scan Gain
Command code:
GET_STATUS
Command name in Litho files: gs
Number of parameters to send: 0
Parameters:
none
Notes:
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gs returns a block of status information to the IP address and port number where the command
originated. In detail the structure looks like this:
[0] u32 — the GET_STATUS command code
[1] u32 — machine state
an FFFF in the HI word means: arrived at spectro stop and waiting
The lower word is coded like this:
IDLE idle
LITHO lithography running
SCAN scan generator running
PREPSCAN scan preparation in progress
SNGLESCN stop scanning after this frame is done
[2] float — scan speed in physunits/second
[3] float — line time in seconds
[4] u32 — the next line draw motion mode
C_SPEED constant speed
SINE_SCAN sine wave speed
NL_LOOKUP nonlinearity table lookup
[5] float — scan rotation angle in deg
[6] float — X scanner position in physunits
[7] float — Y scanner position in physunits
[8] float — X scanner position in Volts
[9] float — Y scanner position in Volts
[10]
float — X scanner position offset in physunits
[11]
float — Y scanner position offset in physunits
The previous two items are offsets in the scan signal. This has nothing to do with the SPM1000
front panel offset knobs. They are separate channels.
[12]
u32 — actual image pixel number on the line
[13]
u32 — actual scan line number
The previous two items are calculated back from the tip position. When the tip is outside the
region defined by SET_BASE these numbers might be negative or bigger than the number of
pixels/lines defined by SET_NPIX_NLIN
[14]
u32 — state of the PEN bit right now
0 means up
0xFFFFFFFF means pen down
[15]
float — X piezo sensitivity as set by SET_MATRIX
[16]
float — Y piezo sensitivity as set by SET_MATRIX
[17]
float — X HV gain as set by SET_MATRIX
[18]
float — Y HV gain as set by SET_MATRIX
[19]
u32 — line draw errors
This shows an error value of 1 when a line draw went off the DAC grid. GET_STATUS resets
this to zero after reading it. An error code of 2 means that one of the SET_MATRIX parameters
was zero and thus the SET_MATRIX has been ignored.
[20]
float — spectroscopy wait time
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[22]
[23]
[24]
[25]
[26]
[27]
[28]
[29]
[30]
[31]
[32]
[33]
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0 means the board is waiting for a SCAN_UNTIL to continue
positive values make the board continue after that many seconds
negative values cause FLAG_A <-> FLAG_B handshaking
u32 — internal flags They are defined as follows
BIT0
SC_ON scan enable?1=Yes,0=No
BIT1
QPD Lithography pen down? 1=Yes, 0=No
BIT2
POSPREP Is the line next to the one currently drawing
prepared? 1=Yes 0=No
BIT3
SPEC_HERE Is this scan line on the spectro grid? 1=Yes
0=No
BIT4
POS_FB_ON Is positioning feedback switched on? 1=Yes
0=No
BIT5
YSCN enable Y scan? 1=Yes0=No
BIT6
NOADC Lock ADC triggers? 1=Yes0=No
BIT7
SINE_LINE Cosine speed line mode for the next line?
BIT8
NL_LOOKUP_LINE use nonlinearity table for this line?
BIT9
IGNORE_USR_SPD ignore speed switch settings? 1=Yes 0
= No
BIT10
QSL Status of the SCAN_LEFT/*RIGHT line during line
draw
BIT11
SPD_TOO_HI speed limited by the scan board due to ADC
conditions
BIT12
LINE_WAITING waiting at a line
BIT13
PC_SET_SPD Who set the actual speed setting: 0= front
panel knob 1= PC
BIT14
INFINIT_TRIG infinite number of trigger groups for
TRIGGER_SERIES
BIT15
MOVING set whenever the scanning LED is on
BIT16
PENDING_TRIG Flag/Wait ISR needs to generate the first
trigger along the line
BIT17
FIBER_FB_RUNS Fiber fb is running
float — scan line length in physunits
scan — Y length in physunits
u32 — Number of pixels
u32 — Number of lines
u32 — number of repetitions for each scan line draw
u32 — On which scan line repetitions do AD triggers see SET_WHERE_AD
u32 — SCANNER_FLAGS see SET_SCANNER_FLAGS
u32 — number of triggers at each image pixel position
float — trigger period at each image pixel position in seconds
float — wait time at the end of a forward scan line [s]
float — wait time at the end of reverse scan line [s]
u32 — actual line repetition number
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[35]
[36]
[37]
[38]
[39]
[40]
[41]
[42]
[43]
[44]
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scanner errors Currently this is always 0. This will give a clue about scan generator
errors
u32 — Lithography instruction pointer value
u32 — Lithography error number
u32 — The last decoded Litho command In case of a bad command the code will be
shown here and [28] shows where in the buffer that happened
float — user gain setting from front panel switch
float — user line time setting from front panel switch These contain the front panel
switch settings. When the user changes the switches these variables will be updated.
The line time shown here is a user wish. When the scan program starts it will try its
best fulfilling this wish. The resulting line time and scan motion speed can be taken
from parameter [2] and [3] of this message. Sending IGNORE_SWITCH 1,
SET_SPEED, SET_LINE_TIME or PREPARE_SCAN command will uncouple
the actual line speed from the front panel switch. An IGNORE_SPEED 0 will make
the board use the switches again. While the speed settings from the switches are
ignored the OVERRIDE LED will light.
u32 — Chassis serial number
u32 — scan board hardware revision number
u32 — Altera firmware revision number
u32 — Kernel revision number
u32 — Scan software revision number
Command code:
GET_DAQ_MODE
Command name in Litho files: gdm
Number of parameters to send: 0
Notes:
This makes the scan board send back its data acquisition mode word. This word contains
parameters for data acquisition for the on-board ADCs. The format of the returned word is the
same as described in
Command code:
SET_DAQ_MODE
Command name in Litho files: sdm
Number of parameters to send: 0
Notes:
This makes the scan board send back its data acquisition mode word. This word contains
parameters for data acquisition for the on-board ADCs. The format of the returned word is the
same as described in
Command code:
SET_DAQ_CHANS
Command name in Litho files: sdc
Number of parameters to send: 1
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Parameters:
u32 channels
Notes:
This command allows to set the data acquisition channels without having to re-configure the data
acquisition. The channels parameter has the same encoding as in
Command code:
SET_POS_FB
Command name in Litho files: spf
Number of parameters to send: 1
Parameters:
u32 mode
Notes:
This command sets the positioning feedback. The modes are:
NO_POS_FB: 0x0 This is the default. The scan board directly outputs to the DACs.
FB_INTEGRATOR: 0x1 This is an I-feedback algorithm that runs in the background of
the scanning. It controls the positioning at any time, not just during scanning. The FB time
constant can be set using SET_POS_FB_TC. Using this algorithm you should not try to
scan faster than 100 ms/line.
Command code:
SET_POS_FB_TC
Command name in Litho files: stc
Number of parameters to send: 1
Parameters:
float gain
Notes:
This sets the feedback time constant for the positioning feedback in FB_INTEGRATOR mode.
The default value that is used on the scan board is 0.02857 s or 1/(35Hz) . This value works for a
NANONICS scanner. For everything else it has to be experimentally determined. Please note:
FB oscillations might be bad for your scanner, be careful with this.
Command code:
SET_DETECTOR_CHAR
Command name in Litho files: sdx
Number of parameters to send: 10
Parameters:
float X_A
float X_B
float X_C
float X_D
float X_E
float Y_A
float Y_B
float Y_C
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float Y_D
float Y_E
Notes:
Most positioning detectors are not linear. This command offers the opportunity to linearize and
decouple the detector using a 3rd order polynomial. The coefficients starting with X_ are for the
X detector, the coefficients starting with Y_ are for the Y detector. The equations (from the
viewpoint of the scan board) are:
and
Physunits are the physical units that you run the scan board in (set by SET_MATRIX). ADC
has Volt units (the range -10V .. 10V) and means the corresponding detector voltage of that
position.
Command code:
READ_DETECTOR_CHAR
Command name in Litho files: rdx
Number of parameters to send: 0
Returns:
float X_A
float X_B
float X_C
float X_D
float X_E
float Y_A
float Y_B
float Y_C
float Y_D
float Y_E
Notes:
This command is used to verify the XY positioning feedback characteristics that gets sent to the
scan board using SET_DETECTOR_CHAR.
Command code:
SETUP_FIBER_FB
Command name in Litho files: setfib
Number of parameters to send: 3
Parameters:
float Setpoint
float TimeConstant
float Interferom_conv
Notes:
This command sets the setpoint and time constant for an interferometer reference channel. This
can drive the reference mirror or the fiber piezo of an interferometer that's used as AFM
detector. The signal from the interferometer preamp needs to be on ADC1 of the scan board. The
fiber piezo drive signal will come out of the ZDAC. The Interferom_conv is just a
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configuration parameter that gets stored on the scan board. It is not used in any internal
calculations but output in the GET_STATUS reply so that SPM32 can have access to this
number.
Command code:
START_FIBER_FB
Command name in Litho files: strtfib
Number of parameters to send: 1
Parameters:
u32 flag
Notes:
This command starts or stops the fiber feedback algorithm with the parameters set up in
SETUP_FIBER_FB. A value of zero in the parameter FLAG will stop the feedback. Everything
else starts the feedback.
Command code:
SETUP_WATCHDOG
Command name in Litho files: setwd
Number of parameters to send: 3
Parameters:
float lowerlimit
float upperlimit
BOOLEAN use_pen_line
Notes:
This command sets the lower and upper limits for a signal watchdog that checks the DSP ADC2
while the fiber feedback runs. The unit for these parameters is Volts. When lowerlimit is smaller
than upperlimit the watchdog checks whether the signal on DSP ADC2 is bigger than lowerlimit
and smaller than upperlimit. When lowerlimit is bigger than upperlimit the algorithm checks
whether the signal is bigger than lowerlimit or smaller than upperlimit. In other words: one way
it tests whether the signal is within the range and the other way it tests whether the signal is
outside the range. When the test fails and use_pen_line is not zero the pen_bit on the DB15
connector goes HI. The algorithm resets the pen_bit when the signal gets back into range. Also
the scanner errors field (field 34) of the GET_STATUS reply will show a 1. Reading the status
resets this error field.
Command code:
SHOW_WATCHDOG
Command name in Litho files: showwd
Number of parameters to send: 0
Notes:
This command displays the upper and lower limit of the signal watchdog algorithm. This will
return : float lower_limit float upper_limit BOOLEAN use_pen_line
Command code:
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Command name in Litho files:
sdr
Number of parameters to send:
2
Parameters:
float Xrate
float Yrate
Examples:
0.01 0.01 sdr
Notes:
This command starts the automatic drift correction algorithm. The digital offsets of the scan
board are moved at the specified rates, given in physical units. If both Xrate and Yrate are zero
then the drift correction algorithm is switched off. The offsets can be returned using the SET
OFFSET command even while the drift correction is active
Line draw operation commands
Command code:
POSITION_ABSOLUTE
Command name in Litho files: pa
Number of parameters to send: 2
Parameters:
float X
float Y
Examples:
pa 20.0 20.0
Notes:
For this to work in physical units the sensitivities using SET_MATRIX must be set.
Command code:
POSITION_RELATIVE
Command name in Litho files: pr
Number of parameters to send: 2
Parameters:
float X
float Y
Examples:
pr 20.0 20.0
Notes:
For this to work in physical units the sensitivities using SET_MATRIX must be set.
Command code:
POSITION_PURE
Command name in Litho files: pp
Number of parameters to send: 2
Parameters:
float X
float Y
Examples:
pp 20.0 20.0
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Notes:
This moves the scanner to the position (X,Y) on the unrotated and un-offset coordinate system.
It is mainly used by SPM32 for range checking. X and Y are given in physical units.
Command code:
POSITION_ABS_EXTD
Command name in Litho files: pae
Number of parameters to send: 11
Parameters:
float X
float Y
float speed
float wait_time: Wait time at line end
u32 flags:
Bit1 PU/PD: 0 — PU
1 — PD,
Bit7 ADC:
0 — YES
1 — NO
Bit11 SCAN_LEFT DIO: 0=LOW 1=HI
u32 TRIGNUM: # AD triggers at each
position
float TR_PERIOD: trigger period in
seconds (a pretty
small number...)
u32 MotionMode: C_SPEED,
SINE_SCAN or
NL_LOOKUP
u32 first_Ints/AD: where first AD
u32 other_Ints/AD: AD trig separation
i32 firstspec : first spectro stop after how
many A/D position
updates
0 — never stop, don't use remainder of
previous line
-1 — use remainder of counts from
previous line
Examples:
pae 20.0 20.0 120000.0 0.01 129 3 0.000001 0
350
Notes:
This function is called by the scan generator. It is the general interface of the line draw section of
the program. Using this an external scan generator could take over the control of the board.
Please note that the X and Y are in internal scan grid units here.
Command code:
SET_WAIT_TIME
Command name in Litho files: swt
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Number of parameters to send: 1
Parameters:
float wait time
Examples:
swt 0.2 -> 200ms wait at line draw ends
swt 0.0 -> no additional wait at line ends
Notes:
Internally this function gets called by POSITION_ABS_EXTD. A negative wait time results in
FLAG_A being set at the end of each line. Drawing continues when FLAG_B is set. Note that
the scanner sets this parameter internally. Use SET_FORWARD_WAIT_TIME and
SET_REVERSE_WAIT_TIME when scanning.
Command code:
SET_LINE_FLAGS
Command name in Litho files: slf
Number of parameters to send: 1
Parameters:
u32 flags
Notes:
Internally this function gets called by POSITION_ABS_EXTD. See the
POSITION_ABS_EXTD description for more details on the flags.
Command code:
SET_TRIGNUM
Command name in Litho files: stnum
Number of parameters to send: 1
Parameters:
u32 TRIGNUM
float TRIG_PERIOD
Notes:
This sets the number of triggers at each A/D position along the next lines. Do not use this for
setting the number of triggers for the next scan. Use SET_SC_TRIGNUM instead. Internally
this function gets called by POSITION_ABS_EXTD. TRIG_PERIOD is the time between
trigger events in seconds
Command code:
SET_MOTION_MODE
Command name in Litho files: smmod
Number of parameters to send: 1
Parameters:
u32 motion_mode
Notes:
Internally this function gets called by POSITION_ABS_EXTD. It sets the motion mode for the
next line to be drawn.
Command code:
SET_FIRST_INTS_AD
Command name in Litho files: sfiad
Number of parameters to send: 1
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Parameters:
u32 first Ints/AD
Notes:
This function sets the number of scanner position updates along the line before the first A/D
trigger sequence is generated. Internally this function gets called by POSITION_ABS_EXTD.
Command code:
SET_OTHER_INTS_AD
Command name in Litho files: soiad
Number of parameters to send: 1
Parameters:
u32 other_Ints/AD
Notes:
This function sets the number of scanner position updates along the line between all other A/D
trigger positions. Internally this function gets called by POSITION_ABS_EXTD.
Command code:
PEN_UP
Command name in Litho files: pu
Number of parameters to send: 0
Notes:
This will deactivate the PEN TTL output. Note that this does not happen until the beginning of
the next line draw.
Command code:
PEN_DOWN
Command name in Litho files: pd
Number of parameters to send: 0
Notes:
This will activate the PEN TTL output. Note that this does not happen until the beginning of the
next line draw.
Command code:
ROTATE_ABSOLUTE
Command name in Litho files: ra
Number of parameters to send: 1
Parameters:
float angle
Examples:
ra 32.31 — rotation angle = 32.31 degree
Notes:
This sets the rotation angle of the image coordinate system with respect to the piezo coordinate
system. A positive angle means image rotation counterclockwise. The angle is given in degree.
This applies to all subsequent line draw actions including scanning.
Command code:
ROTATE_RELATIVE
Command name in Litho files: rr
Number of parameters to send: 1
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Parameters:
float angle_change
Examples:
rr 0.2 — rotate drawing ccw an additonal 0.2 degree
Notes:
This modifies the rotation angle of the image coordinate system with respect to the piezo
coordinate system. A positive angle means image rotation counterclockwise. The angle is given
in degree. This applies to all subsequent line draw actions including scanning.
Command code:
SET_SPEED
Command name in Litho files: ss
Number of parameters to send: 1
Parameters:
float speed ( in physunits/s )
Notes:
Internally this function gets called by POSITION_ABS_EXTD. Speed changes apply to all
subsequent line draws. Note that giving a line time in PREPARE_SCAN will overwrite the
speed setting.
Command code:
SET MATRIX5
Command name in Litho files:
sm5
Number of parameters to send:
5
Parameters:
float SkewAngle
float X Piezo sens
float Y Piezo sens
float HV Gain X
float HV Gain Y
Examples:
13.0 13.0 300.0 300.0 90 sm5
Notes:
This defines the meaning of physunits to the board. The piezo sensitivities are given in
physunits/V, the HV Gains are dimensionless. All other operations are based on physunits so
probably this is one of the first instructions given to the board. The parameter SkewAngle
specifies the angle between the X and Y piezo motion in degrees. In normal microscopes this
angle should be close to 90 degrees.
Command code:
SET_MATRIX
Command name in Litho files: sm
Number of parameters to send: 4
Parameters:
float X_Piezo_sens
float Y_Piezo_sens
float HV_Gain_X
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float HV_Gain_Y
Examples:
sm 300.0 300.0 13.0 13.0
Notes:
This defines the meaning of "physunits" to the board. The piezo sensitivities are given in
physunits/V, the HV_Gains are dimensionless. All other operations are based on physunits so
this should be one of the first instructions given to the board.
Command code:
SET_OFFSET
Command name in Litho files: so
Number of parameters to send: 2
Parameters:
float Xoffs
float Yoffs
Examples:
so 20.0 -30.0
Notes:
This moves the offset of the scan board. The offset coordinates are given in the unrotated
coordinate system (offset moves the center of rotation). Please note: changing the offset also
changes the offset for the current position. The result will be a line draw to the current position
at the new offset. This line draw will be done using the current line parameters.
Command code:
SET OFFSET REL
Command name in Litho files:
sor
Number of parameters to send:
2
Parameters:
float deltaXoffs
float deltaYoffs
Examples:
-30.0 20.0 so
Notes:
This moves the offset of the line draw coordinate system in respect to the piezo coordinate
system. The offset coordinates are given in the unrotated coordinate system (offset moves the
center of rotation) relative to the current offset position. Please note: changing the offset also
changes the offset for the current position. The result will be a line draw to the current position
at the new offset. This line draw will be done using the current line parameters
Command code:
SET_SPEC_WAIT_TIME
Command name in Litho files: sswt
Number of parameters to send: 1
Parameters:
float spectro_wait_time
Notes:
This determines the wait time at each spectro position in table as well as in array mode. At a
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spectro position FLAG_A is set. When the time expires, FLAG_A is cleared automatically for
positive wait times. For negative wait times FLAG_B has to be put high in order to make the
scanner continue.
Command code:
GET_TEST
Command name in Litho files: debug
Number of parameters to send: 0
Notes:
This command returns an array of debugging information. This array can be filled with
debugging information. If unused all elements are zero.
Command code:
TRIGGER_SERIES
Command name in Litho files: trs
Number of parameters to send: 2
Parameters:
float GROUP_PERIOD
float TRIG_PERIOD
u32 NGROUP
u32 TRIG_NUM
Examples:
trs 100e-6 10e-6 6 3
This will generate 6 trigger groups each containing 3 trigger pulses 1 ms apart. The trigger pulse
groups will have a period of 100 ms.
Notes:
This command generates a sequence of trigger groups. GROUP_PERIOD defines the period
time of the trigger groups. NGROUP defines the number of groups. If this is zero triggers will be
generated until told to stop by STOP_SCAN 2. TR_NUM is the number of triggers in each
group. TRIG_PERIOD is the trigger period inside the group.
Command code:
DRAW_ARC
Command name in Litho files: arc
Number of parameters to send: 3
Parameters:
float X0
float Y0
float angle
Notes:
This command draws an arc starting from the current position around the center point (X0,Y0).
The length is determined by the given angle. Negative angle means clockwise.
Command code:
DRAW_ARC_REL
Command name in Litho files: arcr
Number of parameters to send: 3
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float X0
float Y0
float angle
Notes:
This command draws an arc starting from the current position around the center point
(X+dX0,Y+dY0). The coordinates of the center point are given relative to the current position.
The length is determined by the given angle. Negative angle means clockwise.
Command code:
SET_ANGLE_INCREMENT
Command name in Litho files: sai
Number of parameters to send: 1
Parameters:
float angle_increment
Notes:
This allows to set the angle that the arc command connects with a straight line. The default value
is 1 degree. Decreasing the value makes arcs smoother but a little slower.
Command code:
SHAKE_HAND
Command name in Litho files: sh
Number of parameters to send: 2
Parameters:
u32 mode
float wait_time
Notes:
This allows to put wait times and handshake events into lithography files. For mode = 0 or mode
= 1 a positive wait_time will be interpreted as a wait time. For mode = 2 the wait time is
ignored. A negative wait_time will cause handshaking. The handshaking depends on the mode
that has been set:
mode = 0
FLAG_A/FLAG_B handshake (TTL lines )
mode = 1
the command suspends until a SHAKE_HAND command
with mode=2 gets sent
mode = 2
The line draw gets continued
Combined with the positive or negative values that are allowed for wait_time, there are six
possible circumstances that can be executed. They are:
Mode=0 and positive wait_time
wait for wait_time
Mode=0 and negative wait_time
Use FlagA/FlagB method
Mode=1 and positive wait_time
wait for wait_time
Mode=1 and negative wait_time
ethernet handshake (wait for
SHAKE_HAND with mode=2)
Mode=2 and positive wait_time
continue drawing
Mode=2 and negative wait_time
continue drawing
For mode=1 and a negative wait time no UDP packet gets sent. If that is required a
GET_STATUS command needs to be placed in front of this instruction in the litho file.
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Command code:
TRACK_FEATURE
Command name in Litho files: tf
Number of parameters to send: 1
Parameters:
u32 ON_OFF
Notes:
This starts or stops a feature tracking as set up with SETUP_TRACKING. The word ON_OFF
can have these values: 0 -> shut off feature tracking 1 -> start feature tracking
Command code:
SETUP_TRACKING
Command name in Litho files: sft
Number of parameters to send: 10
Parameters:
u32 mode
u32 nconv
float Circle_Radius
float Circle_Freq
float TimeConstant
float ConeHeight
float PhaseShift
float Wait_Time
u32 circles/trace_sample
u32 not_touch_trace
Notes:
This command sets up the feature tracking. In order to start feature tracking mode use the
command TRACK_FEATURE. The feature tracking algorithm draws a circle of radius
Circle_Radius around the current position and calculates the slope in X and in Y direction using
nconv A/D conversions along the circle circumference. Assuming that the feature is a cone of
height ConeHeight and that the circle radius is chosen in way that the circle is at half the cone
height it calculates an X and Y displacement of the cone center with respect to the circle center.
That X and Y displacement is then used to re-position the circle center on top of the cone using
an integrator with the time constant TimeConstant. The cone height can be negative. In that case
the algorithm tracks a depression in the surface.
The mode word contains the number of circles to be drawn in the lower 16 bits. If this number is
zero the algorithm circles until told to stop by a TRACK_FEATURE command. Bit 16 of the
mode word determines whether SET_OFFSET ( bit 16 ==1 ) or the POSITION_ABSOLUTE
(bit 16 == 0) commands are used to re-position the circle center on top of the feature.
The nconv word contains the number of A/D conversions taken along each circle. This number
has to be >= 3, otherwise it will get coerced to 3 by the scan board processor. The Circle_Radius
is given in physical units as defined using SET_MATRIX. Circle_Freq is the number of circles
drawn per second. The TimeConstant is the Feedback integrator time constant given in seconds.
For a stable feedback the relation TimeConstant >= 1/Circle_Freq should be maintained.
PhaseShift gives the phase shift between reference and detected signal. This way for fast
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tracking the phase shift that is induced by the scanner mechanics can be compensated for.
Wait_Time defines a wait time (in seconds) before each circle gets drawn. When the parameter
not_touch_trace is set to a value different from zero this command will not configure ( and thus
not reset ) the tracking trace buffer in external memory. This allows to re-configure the feature
tracking without having to pick up the data of a previous run. Using an unconfigured tracking
buffer means crashing the DSP board.
Command code:
GET_TRACKING_DATA
Command name in Litho files: gtd
Number of parameters to send: 1
Parameters:
u32 how_many
Notes:
This command reads the feature tracking trace out of the scan board external memory. It works
exactly the same as READ_ADC_BUFFER except that the data that is sent back is in 32 bits
IEEE float format.
Command code:
PUSH_SCALE
Command name in Litho files: pushs
Number of parameters to send: 1
Parameters:
float new_scale_factor
Notes:
This command scales the subsequent offset and drawing operations using new_scale_factor. The
factor new_scale_factor also gets put onto a 16 entries deep stack that stores the 15 previous
pushs scaling factors. When more than 16 pushs operations are done without clearing the stack
the first factor will get lost first.
Command code:
POP_SCALE
Command name in Litho files: pops
Number of parameters to send: 0
Notes:
This command pops the scaling stack (puts the second entry into the first position etc... ) This
way the scaling of a previous pushs can be restored. At initialization the scaling factor is 1.0.
When the stack gets underflown it will "produce" scale factors of 1.0.
Command code:
DUMP_SCALING_STACK
Command name in Litho files: dumps
Number of parameters to send: 0
Notes:
This command returns the contents of the scaling stack
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Command code:
SET_REPLAY_MODE
Command name in Litho files: srm
Number of parameters to send: 1
Parameters:
u32 on/off
Notes:
This command enables (on/off <>0) or disables (on/off=0) the replay mode. In replay mode the
line draw subsystem outputs a data stream out of the A/D buffers on the Z DAC while scanning.
This can be used for raster lithography along scan lines. The data can be placed into the A/D
buffers with the wadc command. The buffer gets read one reading per A/D trigger that is
generated by the line draw.
Command code:
SET_REPLAY_FACTOR
Command name in Litho files: srf
Number of parameters to send: 1
Parameters:
float replay_factor
Notes:
This command sets the scale factor that gets multiplied into the ZDAC output signal in Replay
Mode
Command code:
SET DT TRIG PWIDTH
Command name in Litho files:
sdtpw
Number of parameters to send:
1
Parameters:
pulse length
Notes:
This command sets the length in seconds of the trigger pulses that get sent to the DT data
acquisition board in the PC. Please note that the maximum trigger period that can be set in
[prepscan], page 29 or [sctnum], page 31 is twice the number given in “pulse length”.
Command code:
LS_LITHO_MODE
Command name in Litho files: lslm
Number of parameters to send: 1
Parameters:
u32 on/off
Notes:
This command enables (on/off <>0) or disables (on/off = 0) the line start lithography mode. In
this mode the lithography buffer is executed at the beginning of a line draw when a wait time <>
0 is defined.
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Scan layer commands
Command code:
PREPARE_SCAN
Command name in Litho files: prepscan
Number of parameters to send: 13
Parameters:
float baselen scan line length in physunits
float basewidth — scan area height in physunits
float LineTime — scan line draw time (one
way!)
float fwd_wait_tm — stop time after end
of fwd line
float rev_wait_tm — stop time after end
of rev line
u32 npix — number of image pixels on
each line
u32 nlin — number of lines in the scan
u32 motionmode — C_SPEED/
SINE_SCAN/
NL_LOOKUP
u32 rept — # of repetitions for each scan
line
u32 where_AD — A/D triggers on
which repetitions
u32 SCANNER_FLAGS — see
commands.h for coding
u32 TRIGNUM — # of triggers at each
A/D position
float TRIG_PERIOD — trigger period in
seconds
Example:
prepscan 12 12 0.002 0 0 200 200 0 1 3 4 1 7e-6
Notes:
This command sets the parameters for a scan. It then moves the tip position to the scan area
corner defined in SCANNER_FLAGS from where the scan is supposed to start. The motion along
this line will be the speed of the scan as set by LineTime. When the tip position arrives in the
start corner the scanner waits for wait_time_at_start_position seconds before further line draws
can be done. Use the SCAN_UNTIL command then to start a scan. Please note that the speed of
all line draws is set to the speed that corresponds to LineTime. A Linetime of 0.0 will be ignored.
The old scan speed will remain unchanged.
Command code:
SET_REPETITIONS
Command name in Litho files: srep
Number of parameters to send: 1
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Parameters:
u32 rept
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing
Command code:
SET_BASE
Command name in Litho files: sbas
Number of parameters to send: 2
Parameters:
float base_length
float base_width
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing. The
values base_length and base_width give the size of the scan area in physunits.
Command code:
SET_LINETIME
Command name in Litho files: slt
Number of parameters to send: 1
Parameters:
float Line_time
Notes:
Internally this function gets called by PREPARE_SCAN. It sets the scan line time. The scan
line time is the time that just the forward scan line would take, not a forth and back scan... When
other parameters change the system tries to conserve the line time.
Command code:
SET_FWD_WAIT_TIME
Command name in Litho files: sfwt
Number of parameters to send: 1
Parameters:
float wait time at the end of a fwd line [s]
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing. The
time is given in seconds. Negative wait time results in FLAG_A being set at the end of each fwd
line. Scanning continues when FLAG_B is set.
Command code:
SET_REV_WAIT_TIME
Command name in Litho files: srwt
Number of parameters to send: 1
Parameters:
float wait time at the end of a rev line [s]
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing. The
time is given in seconds. Negative wait time results in FLAG_A being set at the end of each rev
line. Scanning continues when FLAG_B is set.
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Command code:
SET_NPIX_NLIN
Command name in Litho files: snp
Number of parameters to send: 2
Parameters:
u32 npix
u32 nlin
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing.
Command code:
SET_SC_MOTMOD
Command name in Litho files: smm
Number of parameters to send: 1
Parameters:
u32 motion_mode
Notes:
This function sets the motion for the scan lines of all following scans. The connection lines will
be constant speed lines.
Command code:
SET_WHERE_AD
Command name in Litho files: swad
Number of parameters to send: 1
Parameters:
u32 where_AD
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing. In
where_AD each bit allows AD trigger generation on a certain line repetition number. Bit 0
means first fwd line, bit 1 means 1st rev line etc. A value of where_AD of 2 means only generate
A/D trigger sequences at the first backward scan. The bits in here are only considered when the
line is drawn. That has to be set using SET_REPETITIONS.
Command code:
SET_SCANNER_FLAGS
Command name in Litho files: ssf
Number of parameters to send: 1
Parameters:
u32 SCANNER_FLAGS
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing. The
scanner flags describe:
Start corner:
Bit 0: 1 — lower
0 — upper
Bit 1: 1 — right
0 — left
Slow scan direction:
Bit 2: 1 — keep
0 — alternate
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Command code:
SET_SC_TRIGNUM
Command name in Litho files: sctnum
Number of parameters to send: 2
Parameters:
u32 TRIGNUM
float TRIG_PERIOD
Notes:
Internally this function gets called by PREPARE_SCAN. It is intended mostly for testing. It
sets the number of A/D triggers generated at each A/D position. Note that this is the value used
by the scan generator. If you set TRIGNUM by using SET_TRIGNUM this will be overwritten
by the SET_SC_TRIGNUM value at the begin of the next scan. TRIG_PERIOD is the time
between trigger events in seconds
Command code:
MOVE_TO_SCAN_START
Command name in Litho files: ms
Number of parameters to send: 0
Notes:
This moves the tip position to the scan area corner defined in SCANNER_FLAGS from where
the scan is supposed to start. The motion along this line will be the speed of the scan as set by
LineTime. Use the SCAN_UNTIL command then to start a scan. Internally this function gets
called by PREPARE_SCAN after all other parameters have been set. A
MOVE_TO_SCAN_START command can be issued at any time. It will then use the
configurations of the last PREPARE_SCAN. When a scan is running a
MOVE_TO_SCAN_START command will stop the current scan at the end of the next
prepared line and then move to the start corner. Please note that the scan generator works in the
background of the line draws that it has "ordered". Any line that got ordered will be drawn. This
means that when you issue a MOVE_TO_SCAN_START command the scanner might actually
draw another line after the current one before it responds.
Command code:
SCAN_UNTIL
Command name in Litho files: su
Number of parameters to send: 1
Parameters:
u32 #image_pixels
Examples:
stpsc 1 ms su 0 — stops the old and starts a new continuous
scan
Notes:
SCAN_UNTIL is the command to use when the scanner should move further along the scan
lines. The value in #image_pixels will tell when the scan gets stopped again. A value of 0 means
continuous scanning. When the scan is stopped the high word of the machine state word in the
GET_STATUS reply is set to 0xffff. The low word still stays at SCAN. SCAN_UNTIL is the
command to use for spectroscopy. SCAN_UNTIL is also used to get a scan running after the
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MOVE_TO_START command. When a SCAN_UNTIL is applied to a running line draw it
sets the number of A/D conversions from the moment the command came in to the next spectro
stop.
Command code:
STOP_SCAN
Command name in Litho files: stpsc
Number of parameters to send: 1
Parameters:
u32 WHERE
Notes:
This command is used to stop the scan in a defined way. The parameter WHERE says where to
abort the scan. The coding is:
EOSCAN stops at the end of a scan frame. Note that this sets the machine state to SNGLESCN
for the rest of the frame
EOLN
stops the scan at the end of this scan line
STOP_NOW
stops the scan immediately, aborting the current line draw
After the STOP_SCAN command the tip position does NOT move to the start corner. You have
to use MOVE_TO_SCAN_START for that. Scans stopped at EOSCAN or EOLN can be
continued using SCAN_UNTIL. For a scan stopped at STOP_NOW this will give unpredictable
results. Use INTERRUPT_SCAN if you want to stop at a previously unknown position along a
scan line and then want to continue scanning.
Command code:
INTERRUPT_SCAN
Command name in Litho files: intsc
Number of parameters to send: 0
Notes:
This command forces a spectroscopy stop at the position of the scanner. Using SCAN_UNTIL
the scan can be continued afterward. As on any spectro stop position the high word of the
machine_state variable is set to 0xffff while the scan is interrupted.
Command code:
STOP_Y_SCAN
Command name in Litho files: stopy
Number of parameters to send: 1
Parameters:
u32 YES_NO — STOP Y = 1 RUN Y = 0
Notes:
This sets or clears a scan generator flag which tells whether the Y line position should be
changed during scanning. This allows to scan a whole image along one line. This might be
interesting for testing the SPM imaging conditions.
Command code:
SET_WHERE_SPEC
Command name in Litho files: sws
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Number of parameters to send: 1
Parameters:
u32 where_spectro
Notes:
Each bit in where_spectro represents a line repetition during scanning. When the bit is set
automatic spectroscopy is allowed on that scan repetition.
Command code:
SPEC_ARRAY_MODE
Command name in Litho files: sam
Number of parameters to send: 4
Parameters:
u32 first_pix,
u32 delta_pix,
u32 firstlin,
u32 deltalin
Notes:
This switches on array mode automatic spectroscopy during the scan line repetitions set by
SET_WHERE_SPEC. Please note that spectroscopy is only possible at points where A/D
conversions are taken. Disabling A/D conversions along a line automatically also disables
spectroscopy. The parameter first_pix gives the pixel position of the first spectroscopy position
from the line start point. The parameter delta_pix gives the separation of the spectro positions
along the line in A/D conversion steps. The parameter firstlin gives the first scan line that
contains spectro stops, counted from the begin of the scan. The parameter deltalin gives the
separation of spectro scan lines along the image. When firstlin < deltalin the spectro positions of
a downward scan and the following upward scan lie exactly on top of each other.
array spectro parameters are:
first_pix — (goes 0 ... npix-1)
delta_pix — (minimum 1)
firstlin — (goes 0 ... nlin-1)
deltalin — (minimum 1)
Command code:
SPEC_TABLE_MODE
Command name in Litho files: stm
Number of parameters to send: depends on table length
Parameters:
spectro position table
Notes:
This command switches on table spectroscopy mode. This allows the placement of spectroscopy
positions on any A/D trigger position on the image. The table contains line numbers (which have
0x0000 in the high word) and position markers for the spectro position on that line. The position
markers are compressed. The Hi word contains a repetition counter and the lower word the
position difference to the previous position or to the line start. Note that there is a position
difference of 1 needed to reach position 0 on the line. A position difference of zero will shut off
spectroscopy for the rest of the line. The table is coded like this:
line number ( has 0x0000 in the high word)
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entry 1, has repetition cntr in Hi word and position X difference in lo word
entry 2, has repetition cntr in Hi word and position X difference in lo word
entry 3, has repetition cntr in Hi word and position X difference in lo word
...
entry n, has repetition cntr in Hi word and position X difference in lo word
line number ( has 0x0000 in the high word)
entry 1, has repetition cntr in Hi word and position X difference in lo word
entry 2, has repetition cntr in Hi word and position X difference in lo word
.
.
.
Example:
0x0
0x00030001
0x05
0x00020003
0x00010004
0x0c
0x00030003
0x00020001
will place spectro stops on
line 0 at positions 0, 1, and 2
line 5 at A/D positions 2, 5, 9 and
line 12 at A/D position 2, 5, 8, 9, 10
The pixel numbers start with 0 and are in decimal notation here.
Command code:
SPEC_NO_MODE
Command name in Litho files: snm
Number of parameters to send: 0
Notes:
This shuts off automatic spectroscopy. SCAN_UNTIL will still do "manual" spectro
positioning.
Command code:
N_LINREP
Command name in Litho files: linrep
Number of parameters to send: 0
Notes:
This command puts the number of the line repetition of the scan generator onto the Lithography
parameter stack. It can be used to make decisions in lithography files that get started at the
beginning of multi line images.
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Lithography commands
Command code:
WRITE_LITHO_BUF
Command name in Litho files: wlb
Number of parameters to send: variable
Parameters:
Instructions to be put into litho buffer
Notes:
This command can not be put into the lithography buffer. That does not make sense. This is the
only command with a variable length. The user has to make sure that the sent packet size does
not exceed the ethernet packet size. Otherwise the packet will be split up by the IP layer of the
control computer and then ignored by the scan board IP routine. Longer instruction sequences
can be downloaded by subsequent WRITE_LITHO_BUF instructions. After the download has
succeeded the lithography pointer points to the first free memory cell after the downloaded
commands. This allows multiple WRITE_LITHO_BUF commands to write more instructions
than what fits into one ethernet buffer. The WRITE_LITHO_BUF instruction returns the
following data structure to the IP address and UDP port number that issued the command:
[0] WRITE_LITHO_BUF code
[1] number of written instructions
[2] remaining free spaces in litho buffer
This is mainly used to confirm that the packet arrived and got processed. (It might get lost in
UDP...)
Command code:
RESET_LITHO_BUF
Command name in Litho files: rlb
Number of parameters to send: 0
Notes:
This is used to stop a running lithography sequence and to set the lithography pointer back to the
begin of the buffer. Please note that the lithography buffer controls both where instructions get
written to by WRITE_LITHO_BUF and where they are read from during execution.
Command code:
JUMP_BUF
Command name in Litho files: jlb
Number of parameters to send: 1
Parameters:
u32 position
Examples:
jlb 0 jumps back to the begin and continues
Notes:
This command simply changes the lithography pointer. This way loops are possible. Conditional
jumps are not supported in this version.
Command code:
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Command name in Litho files: dl
Number of parameters to send: 0
Notes:
This executes the commands in the lithography buffer starting at where the lithography pointer
points to. During lithography execution the lower word of the machine_state word is set to
LITHO.
Command code:
PLUS
Command name in Litho files: +
Number of parameters to send: 0
Notes:
This command adds the two topmost entries on the Lithography stack. It can only be run from
inside a Litho file.
Command code:
JNZ
Command name in Litho files: jnz
Number of parameters to send: 0
Notes:
This command will execute a relative jump inside the lithography buffer. The top of the
parameter stack is the offset of the jump, counted from one position behind the jnz instruction.
Underneath is the counter parameter. When the counter parameter is zero it gets removed from
the stack and no jump is executed. Otherwise the instruction does the relative jump. Please look
at the looptest.lth example file in the C_utilities for an example of this.
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Commands.h file to interpret the command into the 32 bit integer that must be
sent to the DSP board. It does not understand the ASCII string!
/* Global settings and status commands
********************************************/
#define IGNORE_SWITCH
0x01
/* u32 which */
#define IGNORE_SWITCH_LEN
0x02
#define IGN_SPEED
0x0
#define WRITE_Z_DAC
#define WRITE_Z_DAC_LEN
0x02
0x2
/* float output_voltage */
#define BSET_DIO
#define BSET_DIO_LEN
0x03
0x02
/* u32 bit pattern to be set */
#define BCLR_DIO
*/
#define BCLR_DIO_LEN
0x04
/* u32 bit pattern to be cleared
0x02
/* DIO bit definitions */
#define DIO_PAGE
#define DIO_LOOP_INVERT
#define DIO_Z_RETRACT
#define DIO_HOLD_INT
#define SCANNING_LED
#define SCANNING_LED_BIT
#define ADC_CONV_START
#define ADC_CONV_START_BIT
#define OVERRIDE_LED
#define OVERRIDE_LED_BIT
#define SCAN_LEFT_RIGHT
#define SCAN_LEFT_RIGHT_BIT
#define PEN_DOWN_LINE
#define PEN_DOWN_LINE_BIT
0x0001
0x0002
0x0004
0x0008
0x0010
4
0x0020
5
0x0040
6
0x0080
7
0x0100
8
#define TRIGGER_ADC
#define TRIGGER_ADC_LEN
0x05
0x01
/* void */
#define READ_ADC_BUF
#define READ_ADC_BUF_LEN
0x06
0x02
/* u32 how_many samples */
#define GET_STATUS
#define GET_STATUS_LEN
0x07
0x01
/* void */
#define GET_DAQ_MODE
#define GET_DAQ_MODE_LEN
0x08
0x01
/* void */
#define SET_DAQ_MODE
/* channel definitions */
#define ADC1
0x00
0x09
/* u32 buflen, channels, mode */
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#define ADC2
0x01
/* mode word definitions */
#define AD_EXTBUF
0x00
/* 0 -> Buffer in internal memory
1 ->
external buffer */
#define AD_AUTOTRIG
0x01
/* 0 -> needs triggering
1 ->
trigger generated in ADC_isr */
#define AD_AVERAGE
0x02
/* 0 -> one value for each trigger
1 ->
average values until read */
#define POS_INTEGR
0x03
/* Use scan positioning nonlinearity I
feedback algorithm 0 -> no, 1 -> yes */
#define FIBER_FB
0x04
/* Do fiber piezo feedback routine 0 -> no, 1
-> yes */
#define AD_BUF_FULL
0x10
/* 0 -> still space in buffer
1 ->
buffer full */
#define AD_CONVERTING
0x11
/* 0 -> not converting
1 ->
ADCs busy... */
#define SET_DAQ_MODE_LEN
0x04
#define SET_POS_FB
#define NO_POS_FB
#define FB_INTEGRATOR
0x0a
0x0
0x1
#define SET_POS_FB_LEN
0x02
#define SET_POS_FB_TC
#define SET_POS_FB_TC_LEN
0x0b
0x02
/* float TimeConstant */
#define SET_DETECTOR_CHAR
Y_A, Y_B, Y_C, Y_D, Y_E */
#define SET_DETECTOR_CHAR_LEN
0x0c
/* float X_A, X_B, X_C, X_D, X_E,
/* u32 mode */
0x0b
#define READ_DETECTOR_CHAR
0x0d
X_E, Y_A, Y_B, Y_C, Y_D, Y_E */
#define READ_DETECTOR_CHAR_LEN 0x01
/* void, returns X_A, X_B, X_C, X_D,
#define TAKE_DIO
0x0e
/* u32 BIT_PATTERN ... a 1 means SHARC
controls the line. See DIO bit definitions above
*/
#define TAKE_DIO_LEN
0x02
#define SET_Z_SCALE
#define SET_Z_SCALE_LEN
0x0f
0x2
/* float Z_Scale */
#define Z_SET_SPEED
#define Z_SET_SPEED_LEN
0x10
0x2
/* float Z_Sweep_Speed */
#define SETUP_Z_SWEEP
0x11
/* u32 Z_Sweep_Flags, #Sample_groups,
#samples_per_group, ThresholdMode, AD_Channels,
float Z_Sweep_Speed,
PreSampleDelay, TimePerSample, UpperThresholdValue, LowerThresholdValue */
/* Z_Sweep_Flags */
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#define OPEN_FB
#define RESET_ADC
0x0
0x1
#define SETUP_Z_SWEEP_LEN
0xb
#define ABORT_Z_SWEEP
#define ABORT_Z_SWEEP_LEN
0x12
0x1
/* not implemented yet */
/* void */
#define SETUP_FIBER_FB
0x13
/* float setpoint, float
TimeConstant, float Interferom_calib */
#define SETUP_FIBER_FB_LEN
0x4
#define START_FIBER_FB
=> on ) */
#define START_FIBER_FB_LEN
0x14
#define SET_DAQ_CHANS
#define SET_DAQ_CHANS_LEN
0x15
0x2
#define SETUP_WATCHDOG
use_pen_bit */
#define SETUP_WATCHDOG_LEN
0x16
#define SHOW_WATCHDOG
hi, BOOLEAN use_pen_bit */
#define SHOW_WATCHDOG_LEN
0x17
#define WRITE_ADC_BUF
) */
0x18
#define GET_GAINS
0x19
#define GET_GAINS_LEN
#define SET_DRIFT_RATE
#define SET_DRIFT_RATE_LEN
/* FLAG
( 0 => off, everything else
0x2
/* u32 channels */
/* float lo, float hi , u32
0x4
/* void, returns: float lo, float
0x1
/* ( m param_1 . . . param_m -- m
/* void,
float
float
float
float
float
float
returns:
X Offset
X Scan
Y Offset
Y Scan
Z Offset
Z Scan
Gain
Gain
Gain
Gain
Gain
Gain */
0x1
0x1a
0x3
/* float Xdrift Ydrift */
/* line draw operation commands
***************************************************/
#define POSITION_ABSOLUTE
#define POSITION_ABSOLUTE_LEN
0x101
0x03
/* float X, float Y */
#define POSITION_RELATIVE
0x102
/* float X, float Y */
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#define POSITION_RELATIVE_LEN
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0x03
#define POSITION_ABS_EXTD
0x103
/* float X, Y, speed, wait_time;
u32 flags, TRIGNUM, MotionMode, first_Ints/AD,
other_Ints/AD, firstspec */
/*
float X, float Y
-> destination position X and Y
coordinate
float speed,
-> drawing speed of this line
float wait_time
-> Wait time at the end of this
line in seconds
u32 flags
-> flags, saying whether pen up
and whether A/D triggers on this line
Bit1 PU/PD
0 -> PU
1 -> PD,
Bit7 ADC
0 -> YES
1 -> NO
u32 TRIGNUM
-> number of trigger pulses at
each A/D position in case of ADtrig set
float TRIG_PERIOD -> trigger sequence period time in
seconds
u32 MotionMode,
-> motion mode C_SPEED/ SINE_SCAN/
NL_LOOKUP
u32 first_Ints/AD, -> First A/D trigger after how
many scanner updates
u32 other_Ints/AD, -> How many scanner updates
between all other A/D positions along the line
i32 firstspec
-> stop for spectro after how many
A/D trigger positions
firstspec == 0 -> never
stop, don't change remainder of previous line
firstspec == -1 -> use
remainder of previous line
*/
/* position of the parameters for the scanner to call this function */
#define
PAE_X
0x0
#define
PAE_Y
0x1
#define
PAE_SPEED
0x2
#define
PAE_WAIT_TIME
0x3
#define
PAE_FLAGS
0x4
#define
PAE_TRIGNUM
0x5
#define
PAE_TRIG_PERIOD 0x6
#define
PAE_MOTIONMODE
0x7
#define
PAE_FIAD
0x8
#define
PAE_OIAD
0x9
#define PAE_FIRSTSPEC
0xa
#define POSITION_ABS_EXTD_LEN
0x0c
#define SET_WAIT_TIME
#define SET_WAIT_TIME_LEN
0x104
0x02
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/* float wait time */
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#define SET_LINE_FLAGS
#define SET_LINE_FLAGS_LEN
0x105
0x02
/* u32 flags */
#define SET_TRIGNUM
TRIG_PERIOD */
#define SET_TRIGNUM_LEN
0x106
/* u32 TRIGNUM, float
#define SET_MOTION_MODE
#define SET_MOTION_MODE_LEN
0x107
0x02
0x03
/* SET_MOTION_MODE codes */
#define C_SPEED
0
no nonlinearity tables */
#define SINE_SCAN
0x1
*/
#define NL_LOOKUP
0x2
/* u32 motion_mode */
/* no speed variations along the lines,
/* vary the speed with a cosine function
/* use nonlinearity lookup tables */
#define SET_FIRST_INTS_AD
#define SET_FIRST_INTS_AD_LEN
0x108
0x02
/* u32 first Ints/AD */
#define SET_OTHER_INTS_AD
#define SET_OTHER_INTS_AD_LEN
0x109
0x02
/* u32 other_Ints/AD */
#define PEN_UP
#define PEN_UP_LEN
0x10a
0x01
/* void */
#define PEN_DOWN
#define PEN_DOWN_LEN
0x10b
0x01
/* void */
#define ROTATE_ABSOLUTE
#define ROTATE_ABSOLUTE_LEN
0x10c
0x02
/* float angle */
#define ROTATE_RELATIVE
#define ROTATE_RELATIVE_LEN
0x10d
0x02
/* float angle_change*/
#define SET_SPEED
units/s )*/
#define SET_SPEED_LEN
0x10e
/* float speed ( in Matrix
0x02
#define SET_MATRIX
0x10f
/* float X_Piezo_sens,
Y_Piezo_sens [V/phys_unit], float HV_Gain_X, HV_Gain_Y */
#define SET_MATRIX_LEN
0x05
#define SET_OFFSET
#define SET_OFFSET_LEN
0x110
0x03
/* float Xoffs, Yoffs */
#define SET_SPEC_WAIT_TIME
#define SET_SPEC_WAIT_TIME_LEN
0x111
0x02
/* float spectro_wait_time */
#define GET_TEST
0x112
/* void */
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#define GET_TEST_LEN
#define TEST_ARRAY_LEN
0x01
0x4
#define TRIGGER_SERIES
u32 NGROUP TRIG_NUM */
#define TRIGGER_SERIES_LEN
0x113
#define DRAW_ARC
#define DRAW_ARC_LEN
0x114
0x04
/* float GROUP_PERIOD, TRIG_PERIOD
0x05
/* float X0, Y0, angle */
#define SET_ANGLE_INCREMENT
0x115
#define SET_ANGLE_INCREMENT_LEN 0x02
/* float angle_increment */
#define POSITION_PURE
#define POSITION_PURE_LEN
0x116
0x03
/* float X, Y */
#define SHAKE_HAND
#define SHAKE_HAND_LEN
/* modes */
#define FLAG_HS_MODE
#define ENET_HS_MODE
#define ENET_HS_ACK
0x117
0x03
/* u32 mode float time */
#define DRAW_ARC_REL
#define DRAW_ARC_REL_LEN
0x118
0x04
/* float dX0, dY0, angle */
#define TRACK_FEATURE
#define TRACK_FEATURE_LEN
0x119
0x02
/* u32 ON_OFF */
/* ON_OFF */
#define FT_ON
#define FT_OFF
0x1
0x0
#define SETUP_TRACKING
0x11a
0x00
0x01
0x02
/* u32 mode, nconv */
/* float
Circle_Radius,Circle_Freq,TimeConstant,ConeHeight,PhaseOffset,Wait_Time */
/* u32 circ_per_trace_sample,
no_trace_touch */
#define SETUP_TRACKING_LEN
0x0b
/* mode contains the number of circles to run in the bits 0 ... 15 all bits
zero mean circle until told to stop */
#define MOVE_OFFSETS
0x10
/* How to track a feature:
1 =>
use scan offsets
0 => use tip position */
#define PC_SPEED_CTLR
0x11
/* Speed treatment after Ft:
1 =>
just restore speed 0 => restore speed from knobs */
#define PUSH_SCALE
#define PUSH_SCALE_LEN
#define SCALE_STACK_DEPTH
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0x2
0x10
/* float scaling_value */
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#define POP_SCALE
#define POP_SCALE_LEN
0x11c
0x1
/* void */
#define SWEEP_Z_ABSOLUTE
#define SWEEP_Z_ABSOLUTE_LEN
0x11d
0x2
/* float destination */
#define DUMP_SCALE_STACK
#define DUMP_SCALE_STACK_LEN
0x11e
0x1
/* void */
#define SET_OFFSET_REL
#define SET_OFFSET_REL_LEN
0x11f
0x3
/* float dX dY */
#define GET_TRACKING_DATA
#define GET_TRACKING_DATA_LEN
0x120
0x02
/* u32 how_many samples */
#define SET_REPLAY_MODE
#define SET_REPLAY_MODE_LEN
0x121
0x02
/* u32 on? */
#define LS_LITHO_MODE
#define LS_LITHO_MODE_LEN
0x122
0x02
/* u32 on? */
#define SET_REPLAY_FACT
#define SET_REPLAY_FACT_LEN
0x123
0x02
/* float factor */
#define SET_DT_TRIG_PWIDTH
#define SET_DT_TRIG_PWIDTH_LEN
0x124
0x02
/* float pulse width */
#define SET_MATRIX5
0x125
/* float XYAngle, X_Piezo_sens,
#define SET_MATRIX5_LEN
0x06
Y_Piezo_sens [V/phys_unit], float */
/* scan layer commands *************************************************/
#define PREPARE_SCAN
0x201
LineTime, fwd_wait_tm, rev_wait_tm;
/* float baselen, basewidth,
u32 npix, nlin, motionmode, rept,
where_AD, SCANNER_FLAGS, TRIGNUM,
float TRIG_PERIOD,
wait_time_at_start_position */
/*
float baselen
-> length of a scan line in
physical units
float basewidth
-> height of the scan area in
Y in physunits
float LineTime
-> Time to draw one scan line
(one way!)
float fwd_wait_tm -> wait time at the end of a
forward scan line
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Appendices
float rev_wait_tm -> wait time at the end of a
reverse scan line
u32 npix
on each line
-> number of scan trigger positions
u32 nlin
u32 motionmode
NL_LOOKUP
-> number of scan lines.
-> C_SPEED/ SINE_SCAN/
u32 rept
line
-> how many times repeat each scan
u32 where_AD
-> create A/D triggers on which
line repetitions
Bit
Bit
Bit
Bit
0:
1:
2:
3:
1st
1st
2nd
2nd
.
.
.
Bit31:
backward
u32 SCANNER_FLAGS ->
-> upper
-> left
forward
backward
forward
backward
16th
Start corner
Bit 0: 1 -> lower
0
Bit 1: 1 -> right
0
Slow scan direction:
Bit 2: 1 -> keep
-> alternate
u32 TRIGNUM
A/D position
0
-> number of A/D triggers at each
float TRIG_PERIOD -> period of each trigger sequence
in seconds
*/
#define PREPARE_SCAN_LEN
0x0e
#define SET_REPETITIONS
#define SET_REPETITIONS_LEN
0x202
0x02
/* u32 rept */
#define SET_BASE
*/
#define SET_BASE_LEN
0x203
/* float base_length, base_width
#define SET_LINETIME
#define SET_LINETIME_LEN
0x204
0x02
/* float LineTime */
#define SET_FWD_WAIT_TIME
a fwd line [s] */
#define SET_FWD_WAIT_TIME_LEN
0x205
/* float wait time at the end of
#define SET_REV_WAIT_TIME
0x206
RHK Technology
0x03
0x02
/* float wait time at the end of a
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Troy, MI, USA
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rev line [s] */
#define SET_REV_WAIT_TIME_LEN
0x02
#define SET_NPIX_NLIN
#define SET_NPIX_NLIN_LEN
0x207
0x03
/* u32 npix, nlin */
#define SET_SC_MOTMOD
#define SET_SC_MOTMOD_LEN
0x208
0x2
/* u32 scan_line_motion_mode */
#define SET_WHERE_AD
#define SET_WHERE_AD_LEN
0x209
0x02
/* u32 where_AD */
#define SET_SCANNER_FLAGS
#define SET_SCANNER_FLAGS_LEN
0x20a
0x02
/* u32 SCANNER_FLAGS */
#define SET_SC_TRIGNUM
TRIG_PERIOD */
#define SET_SC_TRIGNUM_LEN
0x20b
/* u32 TRIGNUM, float
#define MOVE_TO_SCAN_START
#define MOVE_TO_SCAN_START_LEN
0x20c
0x01
/* void */
#define SCAN_UNTIL
continuous scan */
#define SCAN_UNTIL_LEN
0x20d
/* u32 #image_pixels , when zero
0x03
0x02
#define STOP_SCAN
0x20e
/* u32 WHERE */
#define STOP_SCAN_LEN
0x02
/* note: a scan stopped NOW! cannot be continued */
/* WHERE can be: */
#define EOSCAN
0x0
#define EOLN
0x1
#define STOP_NOW
0x2
#define INTERRUPT_SCAN
#define INTERRUPT_SCAN_LEN
0x20f
0x01
/* void */
#define STOP_Y_SCAN
RUN IT = 0 */
#define STOP_Y_SCAN_LEN
0x210
/* u32 YES_NO : STOP IT = 1
#define SET_WHERE_SPEC
#define SET_WHERE_SPEC_LEN
0x211
0x02
/* u32 where_spectro */
#define SPEC_ARRAY_MODE
firstlin, deltalin */
#define SPEC_ARRAY_MODE_LEN
0x212
/* u32 first_pix, delta_pix,
#define SPEC_TABLE_MODE
/* length not checked */
0x213
RHK Technology
0x02
0x05
/* u32[] spectro table */
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#define SPEC_NO_MODE
#define SPEC_NO_MODE_LEN
0x214
0x01
/* void */
#define N_LINREP
line repetition there */
#define N_LINREP_LEN
0x215
/* only in litho files, returns
0x01
/* lithography stuff
***********************************************************/
#define WRITE_LITHO_BUF
0x301
/* the length is not checked!!! */
/* instructions ... */
#define RESET_LITHO_BUF
0x302
/* void */
#define RESET_LITHO_BUF_LEN
0x01
/* next instructions get written to the begin of the buffer */
#define JUMP_BUF
#define JUMP_BUF_LEN
0x303
0x02
/* i32 position */
/* executes the litho buffer */
#define DO_LITHO
0x304
#define DO_LITHO_LEN
0x01
/* void */
/* puts data onto the litho stack */
#define PUSH_FLOAT
0x305
/* float parameter to push */
#define PUSH_FLOAT_LEN
0x02
#define PUSH_INT
#define PUSH_INT_LEN
0x306
0x02
/* u32 parameter to push */
#define PLUS
#define PLUS_LEN
0x307
0x03
/* u32 u1 u2 */
#define JNZ
#define JNZ_LEN
0x308
0x03
/* i32 where u32 counter */
#define USER_CMD1
#define USER_CMD1_LEN
parameter */
0x0401
0x02
/* Planefit commands */
#define SET_PLANEFIT_MODE
#define SET_PLANEFIT_MODE_LEN
0x0500
0x02
#define
#define
GET_PLANEFIT_MODE
GET_PLANEFIT_MODE_LEN
0x0501
0x01
#define
WRITE_PLANEFIT_PAR
0x0502
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/* u32 parameter */
/* the command itselve and the
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XPMPro User's Manual
Appendices
#define
WRITE_PLANEFIT_PAR_LEN 0x03
#define
#define
READ_PLANEFIT_PAR
READ_PLANEFIT_PAR_LEN
0x0503
0x01
#define
#define
SET_Z_OFFSET
SET_Z_OFFSET_LEN
0x0504
0x02
#define
#define
GET_Z_OFFSET
GET_Z_OFFSET_LEN
0x0505
0x01
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